Delete _static.yaml

Rename static.yaml to _static.yaml

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/static.yaml

@@ -1,43 +0,0 @@
-# Simple workflow for deploying static content to GitHub Pages
-name: Deploy static content to Pages
-
-on:
-  # Runs on pushes targeting the default branch
-  push:
-    branches: ["main"]
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
-  group: "pages"
-  cancel-in-progress: false
-
-jobs:
-  # Single deploy job since we're just deploying
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Setup Pages
-        uses: actions/configure-pages@v3
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
-        with:
-          # Upload entire repository
-          path: 'docs/'
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2

.gitignore

@@ -63,3 +63,4 @@ inst/doc
 drafts/
 
 .DS_Store
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: stRoke
 Title: Clinical Stroke Research
-Version: 23.6.1
+Version: 23.6.2
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))

NAMESPACE

@@ -13,6 +13,7 @@ export(files_filter)
 export(generic_stroke)
 export(index_plot)
 export(label_select)
+export(pase_calc)
 export(quantile_cut)
 export(source_lines)
 export(win_prob)

NEWS.md

@@ -1,3 +1,13 @@
+# stRoke 23.6.2
+
+### Functions:
+
+* NEW: `pase_calc()` function calculates PASE scores from raw questionnaire data. Gives sub scores as well and returns basic data quality and completeness checks. Acknowledges the difference between the scoring manual and the article by Washburn PA. et al. (1999) on including sitting work in the score calculations.
+
+### Data:
+
+* NEW: `pase` sample questionnaire data. Non-identifiable and for use with the `pase_calc()` function.
+
 # stRoke 23.6.1
 
 ### Functions:

R/pase.R

@@ -0,0 +1,32 @@
+#' Data frame with sample data of PASE score questionnaire
+#'
+#' Contains non-identifiable organic trial data.
+#' Sample data labels are in Danish.
+#'
+#' @format A data frame with 200 rows and 21 variables:
+#' \describe{
+#'   \item{sample_pase01}{item 01, factor}
+#'   \item{sample_pase01b}{item 01b, factor}
+#'   \item{sample_pase02}{item 02, factor}
+#'   \item{sample_pase02a}{item 02a, factor}
+#'   \item{sample_pase03}{item 03, factor}
+#'   \item{sample_pase03b}{item 03b, factor}
+#'   \item{sample_pase04}{item 04, factor}
+#'   \item{sample_pase04b}{item 04b, factor}
+#'   \item{sample_pase05}{item 05, factor}
+#'   \item{sample_pase05b}{item 05b, factor}
+#'   \item{sample_pase06}{item 06, factor}
+#'   \item{sample_pase06b}{item 06b, factor}
+#'   \item{sample_pase07}{item 07, factor}
+#'   \item{sample_pase08}{item 08, factor}
+#'   \item{sample_pase09a}{item 09a, factor}
+#'   \item{sample_pase09b}{item 09b, factor}
+#'   \item{sample_pase09c}{item 09c, factor}
+#'   \item{sample_pase09d}{item 09d, factor}
+#'   \item{sample_pase10}{item 10, factor}
+#'   \item{sample_pase10a}{item 10a, numeric}
+#'   \item{sample_pase10b}{item 10b, factor}
+#' }
+#' @usage data(pase)
+"pase"
+

R/pase_calc.R

@@ -0,0 +1,171 @@
+#' PASE score calculator
+#' 
+#' Calculates PASE score from raw questionnaire data.
+#' @param ds data set
+#' @param adjust_work flag to set whether to include 10b type 1. 
+#' Default is TRUE.
+#'
+#' @return data.frame
+#' @export
+#' @details
+#' Labelling should be as defined by the questionnaire.
+#' 02-06 should start with 0:3, 02a-06b should start with 1:4.
+#' 
+#' ## Regarding work scoring
+#' The score calculation manual available for the PASE questionnaire, all types
+#' of work should be included. According to the article by 
+#' Washburn RA. et al (1999) sitting work is not included in the item 10 score.
+#' This differentiation is added with the option to set `adjust_work` to
+#' exclude item 10b category 1 work (set `TRUE`).
+#' 
+#' ## Regarding output
+#' Output includes sub scores as well as sums, but also to columns assessing data 
+#' quality and completeness. If any field has not been filled, `score_incompletes`
+#' will return `TRUE`. If all measures are missing `score_missings` is `TRUE`.
+#' If `adjust_work==TRUE`, 10b has to be filled, or `score_incompletes` will be
+#' set `TRUE`.
+#' 
+#' @examples
+#' summary(pase_calc(stRoke::pase)[,13])
+#' 
+pase_calc <- function(ds, adjust_work = FALSE) {
+  
+  if (ncol(ds) != 21) stop("supplied data set has to contain exactly 21 columns")
+  
+  pase <- ds
+  
+  ## Classify all as characters
+  ## Labelling should be as defined by the questionnaire.
+  ## 02-06 should start with 0:3, 02a-06b should start with 1:4.
+  
+  pase <- do.call(data.frame, lapply(pase, as.character))
+  
+  ## Missings and incompletes
+  missings <- apply(apply(ds, 2, is.na), 1, all)
+  incompletes <-
+    apply(sapply(ds[, c(1, 3, 5, 7, 9, 11, 13:20)], function(x) {
+      x == "Not available" | is.na(x)
+    }), 1, any)
+  
+  names(pase) <- c(
+    "pase01",
+    "pase01b",
+    "pase02",
+    "pase02a",
+    "pase03",
+    "pase03b",
+    "pase04",
+    "pase04b",
+    "pase05",
+    "pase05b",
+    "pase06",
+    "pase06b",
+    "pase07",
+    "pase08",
+    "pase09a",
+    "pase09b",
+    "pase09c",
+    "pase09d",
+    "pase10",
+    "pase10a",
+    "pase10b"
+  )
+  
+  pase_list <- lapply(unique(substr(names(pase), 5, 6)), function(x) {
+    pase[grepl(x, substr(names(pase), 5, 6))]
+  })
+  names(pase_list) <- unique(substr(names(pase), 5, 6))
+  
+  ## PASE 2-6
+  
+  pase_weigths <- list(
+    "1" = c(
+      "1" = 0.11,
+      "2" = 0.32,
+      "3" = 0.64,
+      "4" = 1.07
+    ),
+    "2" = c(
+      "1" = 0.25,
+      "2" = 0.75,
+      "3" = 1.5,
+      "4" = 2.5
+    ),
+    "3" = c(
+      "1" = 0.43,
+      "2" = 1.29,
+      "3" = 2.57,
+      "4" = 4.29
+    )
+  )
+  
+  ## Multiplication factors
+  pase_multip_26 <- c(20, 21, 23, 23, 30)
+  
+  pase_score_26 <- lapply(seq_along(pase_list[2:6]), function(x) {
+    df <- pase_list[2:6][[x]]
+    score <- c()
+    
+    ## =====================
+    ## Checking labelling
+    if (!all(range(suppressWarnings(as.numeric(substr(
+      df[, 1], 1, 1
+    ))), na.rm = TRUE) == c(0, 3))) {
+      stop("Labelling of 02-06 should start with a number ranging 1-4")
+    }
+    ## =====================
+    
+    for (i in seq_len(nrow(df))) {
+      # Setting categories from numbers
+      n1 <- suppressWarnings(as.numeric(substr(df[, 1][i], 1, 1)))
+      
+      # Using if statement to calculate row wise
+      if (n1 %in% c(1:3)) {
+        # Second category
+        n2 <- suppressWarnings(as.numeric(substr(df[, 2][i], 1, 1)))
+        score[i] <- pase_weigths[[n1]][n2] * pase_multip_26[x] 
+        
+      } else if (n1 %in% 0) {
+        score[i] <- 0
+      } else {
+        score[i] <- NA
+      }
+    }
+    score
+  })
+  
+  names(pase_score_26) <- paste0("score_", names(pase_list[2:6]))
+  
+  ## PASE 7-9d
+  pase_multip_79 <- c(25, 25, 30, 36, 20, 35)
+  
+  pase_score_79 <-
+    data.frame(t(t(
+      sapply(Reduce(cbind,pase_list[7:9]),function(j){
+        grepl("[Jj]a",j)
+      }) + 0 # short hand logic to numeric
+    ) * pase_multip_79))
+  
+  names(pase_score_79) <-
+    paste0("score_", sub("pase", "", names(pase_score_79)))
+  
+  ## PASE 10
+  ## Completely ignores if 10b is not completed
+  pase_score_10 <- 21 * suppressWarnings(as.numeric(pase_list[[10]][[2]])) / 7
+  
+  if (adjust_work){
+    # Only includes work time if 10b is != 1
+    pase_score_10[substr(pase_list[[10]][[3]],1,1) == "1"] <- 0
+    # Consequently consider "Not available" in 10b as incomplete
+    incompletes[ds[,21] == "Not available" & !incompletes & !is.na(incompletes)] <- TRUE
+  }
+  
+  pase_score <- cbind(pase_score_26, pase_score_79, pase_score_10)
+  
+  data.frame(
+    pase_score,
+    score_sum = rowSums(pase_score, na.rm = TRUE),
+    score_missings = missings,
+    score_incompletes = incompletes
+  )
+}

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: ~
+url: https://agdamsbo.github.io/stRoke/
 template:
   bootstrap: 5
 

docs/404.html

@@ -1,104 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>Page not found (404) • stRoke</title>
-<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
-<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
-<meta property="og:image" content="/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
-
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="index.html">stRoke</a>
-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">23.6.1</small>
-
-    
-    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
-      <span class="navbar-toggler-icon"></span>
-    </button>
-
-    <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/ds2dd.html">ds2dd</a>
-    <a class="dropdown-item" href="articles/toolbox.html">Toolbox</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
-</li>
-      </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/agdamsbo/stRoke/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-      </ul>
-</div>
-
-    
-  </div>
-</nav><div class="container template-title-body">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="logo.png" class="logo" alt=""><h1>Page not found (404)</h1>
-      
-    </div>
-
-Content not found. Please use links in the navbar.
-
-  </main>
-</div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
-
-    </footer>
-</div>
-
-  
-
-  
-
-  </body>
-</html>

docs/LICENSE-text.html

@@ -1,293 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • stRoke</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<pre>GNU AFFERO GENERAL PUBLIC LICENSE
-Version 3, 19 November 2007
-
-Copyright (C) 2007 Free Software Foundation, Inc. &lt;http://fsf.org/&gt;
-
-Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
-
-                            Preamble
-
-The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software.
-
-The licenses for most software and other practical works are designed to take away your freedom to share and change the works.  By contrast, our General Public Licenses are intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users.
-
-When we speak of free software, we are referring to freedom, not price.  Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
-
-Developers that use our General Public Licenses protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License which gives you legal permission to copy, distribute and/or modify the software.
-
-A secondary benefit of defending all users' freedom is that improvements made in alternate versions of the program, if they receive widespread use, become available for other developers to incorporate.  Many developers of free software are heartened and encouraged by the resulting cooperation.  However, in the case of software used on network servers, this result may fail to come about. The GNU General Public License permits making a modified version and letting the public access it on a server without ever releasing its source code to the public.
-
-The GNU Affero General Public License is designed specifically to ensure that, in such cases, the modified source code becomes available to the community.  It requires the operator of a network server to provide the source code of the modified version running there to the users of that server.  Therefore, public use of a modified version, on a publicly accessible server, gives the public access to the source code of the modified version.
-
-An older license, called the Affero General Public License and published by Affero, was designed to accomplish similar goals.  This is a different license, not a version of the Affero GPL, but Affero has released a new version of the Affero GPL which permits relicensing under this license.
-
-The precise terms and conditions for copying, distribution and modification follow.
-
-                       TERMS AND CONDITIONS
-
-0. Definitions.
-
-"This License" refers to version 3 of the GNU Affero General Public License.
-
-"Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
-
-"The Program" refers to any copyrightable work licensed under this License.  Each licensee is addressed as "you".  "Licensees" and "recipients" may be individuals or organizations.
-
-To "modify" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy.  The resulting work is called a "modified version" of the earlier work or a work "based on" the earlier work.
-
-A "covered work" means either the unmodified Program or a work based on the Program.
-
-To "propagate" a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy.  Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
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-To "convey" a work means any kind of propagation that enables other parties to make or receive copies.  Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
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-An interactive user interface displays "Appropriate Legal Notices" to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License.  If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
-
-1. Source Code.
-The "source code" for a work means the preferred form of the work for making modifications to it.  "Object code" means any non-source form of a work.
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-A "Standard Interface" means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
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-The "System Libraries" of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form.  A "Major Component", in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
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-The "Corresponding Source" for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities.  However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work.  For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those
-subprograms and other parts of the work.
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-The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
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-The Corresponding Source for a work in source code form is that same work.
-
-2. Basic Permissions.
-All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met.  This License explicitly affirms your unlimited permission to run the unmodified Program.  The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work.  This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
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-You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force.  You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright.  Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
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-Conveying under any other circumstances is permitted solely under the conditions stated below.  Sublicensing is not allowed; section 10 makes it unnecessary.
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-3. Protecting Users' Legal Rights From Anti-Circumvention Law.
-No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
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-When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
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-4. Conveying Verbatim Copies.
-You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
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-You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
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-5. Conveying Modified Source Versions.
-You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:
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-    a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
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-    b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7.  This requirement modifies the requirement in section 4 to "keep intact all notices".
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-    c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy.  This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged.  This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
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-    d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
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-A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an "aggregate" if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit.  Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
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-6. Conveying Non-Source Forms.
-You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
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-    a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
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-    b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
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-    c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source.  This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
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-    d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge.  You need not require recipients to copy the Corresponding Source along with the object code.  If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source.  Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
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-    e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
-
-A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.
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-A "User Product" is either (1) a "consumer product", which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling.  In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage.  For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product.  A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.
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-"Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source.  The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
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-If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information.  But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
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-The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed.  Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
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-Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
-
-7. Additional Terms.
-"Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law.  If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
-
-When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it.  (Additional permissions may be written to require their own removal in certain cases when you modify the work.)  You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
-
-Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
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-    a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
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-    b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
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-    c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
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-    d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
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-    e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
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-    f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.
-
-All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10.  If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term.  If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
-
-If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
-
-Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
-
-8. Termination.
-
-You may not propagate or modify a covered work except as expressly provided under this License.  Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
-
-However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
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-Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
-
-Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License.  If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
-
-9. Acceptance Not Required for Having Copies.
-
-You are not required to accept this License in order to receive or run a copy of the Program.  Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance.  However, nothing other than this License grants you permission to propagate or modify any covered work.  These actions infringe copyright if you do not accept this License.  Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
-
-10. Automatic Licensing of Downstream Recipients.
-
-Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License.  You are not responsible for enforcing compliance by third parties with this License.
-
-An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations.  If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
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-You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License.  For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
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-11. Patents.
-
-A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based.  The work thus licensed is called the contributor's "contributor version".
-
-A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version.  For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
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-Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
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-In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement).  To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
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-If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent
-license to downstream recipients.  "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
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-If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
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-A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License.  You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
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-Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
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-12. No Surrender of Others' Freedom.
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-If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License.  If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may
-not convey it at all.  For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
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-13. Remote Network Interaction; Use with the GNU General Public License.
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-Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding Source from a network server at no charge, through some standard or customary means of facilitating copying of software.  This Corresponding Source shall include the Corresponding Source for any work covered by version 3 of the GNU General Public License that is incorporated pursuant to the following paragraph.
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-Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU General Public License into a single combined work, and to convey the resulting work.  The terms of this License will continue to apply to the part which is the covered work, but the work with which it is combined will remain governed by version 3 of the GNU General Public License.
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-14. Revised Versions of this License.
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-The Free Software Foundation may publish revised and/or new versions of the GNU Affero General Public License from time to time.  Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
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-To do so, attach the following notices to the program.  It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
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-     &lt;one line to give the program's name and a brief idea of what it does.&gt;
-     Copyright (C) &lt;year&gt;  &lt;name of author&gt;
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docs/articles/Simple REDCap workflow.html

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-      <img src="" class="logo" alt=""><h1>Simple REDCap workflow</h1>
-            
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-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/vignettes/Simple%20REDCap%20workflow.Rmd" class="external-link"><code>vignettes/Simple REDCap workflow.Rmd</code></a></small>
-      <div class="d-none name"><code>Simple REDCap workflow.Rmd</code></div>
-    </div>
-
-    
-    
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://agdamsbo.github.io/stRoke/" class="external-link">stRoke</a></span><span class="op">)</span></span></code></pre></div>
-<div class="section level2">
-<h2 id="working-with-data-from-redcap">Working with data from REDCap<a class="anchor" aria-label="anchor" href="#working-with-data-from-redcap"></a>
-</h2>
-<p><a href="">REDCap</a> is an excellent tool for clinical data
-acquisition and storage. It is widely used world wide and is the
-standard tool for medical research data in Denmark.</p>
-<p>In the case of analysing data directly whole storing data in REDCap,
-the API functionality is very convenient and secure, as you are not
-storing (possibly) sensitive data permanently on your computer.</p>
-<p>When using the “events” or “repeated instruments” functionality of
-REDCap, the data storage format is a little confusing to work with, when
-being accustomed to tidy data.</p>
-<p>The <a href=""><code>library(REDCapR)</code></a> provides a simple
-way of working with data, however, the package just exports data in
-standard format.</p>
-<div class="section level3">
-<h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
-</h3>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ouhscbbmc.github.io/REDCapR/" class="external-link">REDCapR</a></span><span class="op">)</span></span>
-<span><span class="co"># Returns the variables "record_id" and "age".</span></span>
-<span><span class="va">ds_some_vars</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a></span><span class="op">(</span></span>
-<span>  redcap_uri   <span class="op">=</span> <span class="st">"https://redcap.au.dk/api/"</span>,  <span class="co"># This is the address for projects at the AU-server</span></span>
-<span>  token        <span class="op">=</span> <span class="st">"YOUR_API_KEY_GOES_HERE"</span>,</span>
-<span>  fields       <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>, <span class="st">"age"</span><span class="op">)</span></span>
-<span><span class="op">)</span><span class="op">$</span><span class="va">data</span> </span>
-<span></span>
-<span><span class="co"># Return only records with IDs of 1 and 4</span></span>
-<span><span class="va">ds_some_rows</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a></span><span class="op">(</span></span>
-<span>  redcap_uri   <span class="op">=</span> <span class="st">"https://redcap.au.dk/api/"</span>,  <span class="co"># This is the address for projects at the AU-server</span></span>
-<span>  token        <span class="op">=</span> <span class="st">"YOUR_API_KEY_GOES_HERE"</span>,</span>
-<span>  records      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">4</span><span class="op">)</span></span>
-<span><span class="op">)</span><span class="op">$</span><span class="va">data</span></span></code></pre></div>
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-    
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://agdamsbo.github.io/stRoke/" class="external-link">stRoke</a></span><span class="op">)</span></span></code></pre></div>
-<div class="section level2">
-<h2 id="a-toolbox">A toolbox<a class="anchor" aria-label="anchor" href="#a-toolbox"></a>
-</h2>
-<p>My own toolbox in my small workshop is a mix of some old, worn, well
-proven tools and some newcomers. This package should be seen as
-something like that.</p>
-<p>I have tried to collect tools and functions from other packages that
-I use regularly in addition to functions that I have written myself to
-fill use cases, that I have not been able to find solutions to
-elsewhere.</p>
-<p>In documenting and testing the package, I have used <a href="https://platform.openai.com/overview" class="external-link">OpenAI’s</a> chatgpt with <a href="https://jameshwade.github.io/gpttools/" class="external-link">gpttools</a>. The chatgpt
-is an interesting tool, that is in no way perfect, but it helps with
-tedious tasks. Both <code>gpttools</code> and <a href="https://michelnivard.github.io/gptstudio/" class="external-link"><code>gptstudio</code></a>
-are interesting implementations in R and RStudio.</p>
-<div class="section level3">
-<h3 id="cpr-intro">CPR manipulations<a class="anchor" aria-label="anchor" href="#cpr-intro"></a>
-</h3>
-<p>Note that, if handled, CPR numbers (social security numbers) should
-be handled with care as they a considered highly sensitive data.</p>
-<p>The CPR number is structured as <em>DDMMYY-XXXX</em>, with the 1st
-<em>X</em> designating decade of birth, the last <em>X</em> designate
-binary gender (not biological sex) dependent on even/uneven as
-female/male, and the last for digits are used in a modulus calculation
-to verify the validity of the CPR number. Foreigners and unidentified
-persons are given temporary CPR numbers including letters.</p>
-<p>More information can be found on <a href="https://cpr.dk" class="external-link">cpr.dk</a>.</p>
-<p>Note, that all CPR numbers used in examples are publicly known or
-non-organic.</p>
-<div class="section level4">
-<h4 id="age_calc">age_calc()<a class="anchor" aria-label="anchor" href="#age_calc"></a>
-</h4>
-<p>The age_calc() function was created as a learning exercise and
-functions similarly to <code><a href="https://lubridate.tidyverse.org/reference/time_length.html" class="external-link">lubridate::time_length()</a></code>.</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="op">(</span><span class="va">age</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/age_calc.html">age_calc</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"1945-10-23"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-09-30"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 72.93699</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">trunc</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 72</span></span></code></pre></div>
-</div>
-<div class="section level4">
-<h4 id="cpr_check">cpr_check()<a class="anchor" aria-label="anchor" href="#cpr_check"></a>
-</h4>
-<p>Checks validity of CPR numbers according to the <a href="https://cpr.dk/cpr-systemet/opbygning-af-cpr-nummeret" class="external-link">modulus 11
-rule</a>. Note that due to limitations in the possible available CPR
-numbers, this rule <a href="https://cpr.dk/cpr-systemet/personnumre-uden-kontrolciffer-modulus-11-kontrol" class="external-link">does
-not apply to all CPR numbers after 2007</a>.</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/cpr_check.html">cpr_check</a></span><span class="op">(</span></span>
-<span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
-<span>    <span class="st">"2310450637"</span>,</span>
-<span>    <span class="st">"010190-2000"</span>,</span>
-<span>    <span class="st">"010115-4000"</span>,</span>
-<span>    <span class="st">"300450-1030"</span>,</span>
-<span>    <span class="st">"010150-4021"</span>,</span>
-<span>    <span class="st">"010150-4AA1"</span></span>
-<span>  <span class="op">)</span></span>
-<span><span class="op">)</span></span>
-<span><span class="co">#&gt; OBS: as per 2007 not all valid CPR numbers apply to modulus 11 rule.</span></span>
-<span><span class="co">#&gt;     </span></span>
-<span><span class="co">#&gt; See the vignette 'Toolbox'</span></span>
-<span><span class="co">#&gt; Warning in matrix(as.numeric(unlist(strsplit(cpr_short, ""))), nrow = 10): NAs</span></span>
-<span><span class="co">#&gt; introduced by coercion</span></span>
-<span><span class="co">#&gt; [1]  TRUE FALSE FALSE FALSE FALSE    NA</span></span></code></pre></div>
-<p>Including CPR numbers with letters gives a warning and
-<code>NA</code>, as it can not be checked by the modulus 11 function.
-Should be used with care, see the message.</p>
-</div>
-<div class="section level4">
-<h4 id="cpr_dob">cpr_dob()<a class="anchor" aria-label="anchor" href="#cpr_dob"></a>
-</h4>
-<p>Extracts date of birth (DOB) from a CPR number. Accounts for the
-decade of birth. <a href="#cpr-intro">See earlier</a>.</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/cpr_dob.html">cpr_dob</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
-<span>  <span class="st">"2310450637"</span>,</span>
-<span>  <span class="st">"010190-2000"</span>,</span>
-<span>  <span class="st">"010115-4000"</span>,</span>
-<span>  <span class="st">"300450-1030"</span>,</span>
-<span>  <span class="st">"010150-4021"</span></span>
-<span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] "23-10-1945" "01-01-1990" "01-01-2015" "30-04-1950" "01-01-1950"</span></span></code></pre></div>
-</div>
-<div class="section level4">
-<h4 id="cpr_female">cpr_female()<a class="anchor" aria-label="anchor" href="#cpr_female"></a>
-</h4>
-<p>Gives logical vector of whether female gender from last digit of
-CPR.</p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="fu"><a href="../reference/cpr_female.html">cpr_female</a></span><span class="op">(</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="../reference/cprs.html">cprs</a></span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; FALSE  TRUE </span></span>
-<span><span class="co">#&gt;    98   102</span></span></code></pre></div>
-</div>
-</div>
-<div class="section level3">
-<h3 id="plotting">Plotting<a class="anchor" aria-label="anchor" href="#plotting"></a>
-</h3>
-<div class="section level4">
-<h4 id="ci_plot">ci_plot()<a class="anchor" aria-label="anchor" href="#ci_plot"></a>
-</h4>
-<p>Plots odds ratios with 95 % confidence intervals. Performs binary
-logistic regression for outcome factors with two (2) levels and ordinal
-logistic regression for outcome factors with more than two levels. Mind
-relevant assumptions.</p>
-<p>Outputs ggplot element for further manipulation.</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">talos</span><span class="op">)</span></span>
-<span><span class="va">talos</span><span class="op">[</span>, <span class="st">"mrs_1"</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">talos</span><span class="op">[</span>, <span class="st">"mrs_1"</span><span class="op">]</span>, ordered <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="fu"><a href="../reference/ci_plot.html">ci_plot</a></span><span class="op">(</span></span>
-<span>  ds <span class="op">=</span> <span class="va">talos</span>,</span>
-<span>  x <span class="op">=</span> <span class="st">"rtreat"</span>,</span>
-<span>  y <span class="op">=</span> <span class="st">"mrs_1"</span>,</span>
-<span>  vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hypertension"</span>, <span class="st">"diabetes"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span>
-<span><span class="co">#&gt; Waiting for profiling to be done...</span></span></code></pre></div>
-<p><img src="toolbox_files/figure-html/ci_plot-example-1.png" width="700"></p>
-</div>
-<div class="section level4">
-<h4 id="generic_stroke">generic_stroke()<a class="anchor" aria-label="anchor" href="#generic_stroke"></a>
-</h4>
-<p>For learning purposes. Uses annonymized data from the <a href="https://doi.org/10.1161/STROKEAHA.117.020067" class="external-link">TALOS trial</a> to
-output a Table 1 (with <code><a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_summary.html" class="external-link">gtsummary::tbl_summary()</a></code>), plotting
-the so-called grotta-bars based on mRS scores (with
-<code><a href="https://rdrr.io/pkg/rankinPlot/man/grottaBar.html" class="external-link">rankinPlot::grottaBar()</a></code>) and a ordinal logistic regression
-model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a></code>).</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/generic_stroke.html">generic_stroke</a></span><span class="op">(</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="../reference/talos.html">talos</a></span>,</span>
-<span>               <span class="st">"rtreat"</span>,</span>
-<span>               <span class="st">"mrs_6"</span>,</span>
-<span>               variables <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hypertension"</span>, <span class="st">"diabetes"</span>, <span class="st">"civil"</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Waiting for profiling to be done...</span></span>
-<span><span class="co">#&gt; $`Table 1`</span></span>
-<span><span class="co">#&gt; &lt;div id="iuwzpsksfr" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"&gt;</span></span>
-<span><span class="co">#&gt;   &lt;style&gt;#iuwzpsksfr table {</span></span>
-<span><span class="co">#&gt;   font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';</span></span>
-<span><span class="co">#&gt;   -webkit-font-smoothing: antialiased;</span></span>
-<span><span class="co">#&gt;   -moz-osx-font-smoothing: grayscale;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr thead, #iuwzpsksfr tbody, #iuwzpsksfr tfoot, #iuwzpsksfr tr, #iuwzpsksfr td, #iuwzpsksfr th {</span></span>
-<span><span class="co">#&gt;   border-style: none;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr p {</span></span>
-<span><span class="co">#&gt;   margin: 0;</span></span>
-<span><span class="co">#&gt;   padding: 0;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_table {</span></span>
-<span><span class="co">#&gt;   display: table;</span></span>
-<span><span class="co">#&gt;   border-collapse: collapse;</span></span>
-<span><span class="co">#&gt;   line-height: normal;</span></span>
-<span><span class="co">#&gt;   margin-left: auto;</span></span>
-<span><span class="co">#&gt;   margin-right: auto;</span></span>
-<span><span class="co">#&gt;   color: #333333;</span></span>
-<span><span class="co">#&gt;   font-size: 16px;</span></span>
-<span><span class="co">#&gt;   font-weight: normal;</span></span>
-<span><span class="co">#&gt;   font-style: normal;</span></span>
-<span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
-<span><span class="co">#&gt;   width: auto;</span></span>
-<span><span class="co">#&gt;   border-top-style: solid;</span></span>
-<span><span class="co">#&gt;   border-top-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-top-color: #A8A8A8;</span></span>
-<span><span class="co">#&gt;   border-right-style: none;</span></span>
-<span><span class="co">#&gt;   border-right-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   border-bottom-style: solid;</span></span>
-<span><span class="co">#&gt;   border-bottom-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-bottom-color: #A8A8A8;</span></span>
-<span><span class="co">#&gt;   border-left-style: none;</span></span>
-<span><span class="co">#&gt;   border-left-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-left-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_caption {</span></span>
-<span><span class="co">#&gt;   padding-top: 4px;</span></span>
-<span><span class="co">#&gt;   padding-bottom: 4px;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_title {</span></span>
-<span><span class="co">#&gt;   color: #333333;</span></span>
-<span><span class="co">#&gt;   font-size: 125%;</span></span>
-<span><span class="co">#&gt;   font-weight: initial;</span></span>
-<span><span class="co">#&gt;   padding-top: 4px;</span></span>
-<span><span class="co">#&gt;   padding-bottom: 4px;</span></span>
-<span><span class="co">#&gt;   padding-left: 5px;</span></span>
-<span><span class="co">#&gt;   padding-right: 5px;</span></span>
-<span><span class="co">#&gt;   border-bottom-color: #FFFFFF;</span></span>
-<span><span class="co">#&gt;   border-bottom-width: 0;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_subtitle {</span></span>
-<span><span class="co">#&gt;   color: #333333;</span></span>
-<span><span class="co">#&gt;   font-size: 85%;</span></span>
-<span><span class="co">#&gt;   font-weight: initial;</span></span>
-<span><span class="co">#&gt;   padding-top: 3px;</span></span>
-<span><span class="co">#&gt;   padding-bottom: 5px;</span></span>
-<span><span class="co">#&gt;   padding-left: 5px;</span></span>
-<span><span class="co">#&gt;   padding-right: 5px;</span></span>
-<span><span class="co">#&gt;   border-top-color: #FFFFFF;</span></span>
-<span><span class="co">#&gt;   border-top-width: 0;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_heading {</span></span>
-<span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
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-<span><span class="co">#&gt;   border-left-style: none;</span></span>
-<span><span class="co">#&gt;   border-left-width: 1px;</span></span>
-<span><span class="co">#&gt;   border-left-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   border-right-style: none;</span></span>
-<span><span class="co">#&gt;   border-right-width: 1px;</span></span>
-<span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_bottom_border {</span></span>
-<span><span class="co">#&gt;   border-bottom-style: solid;</span></span>
-<span><span class="co">#&gt;   border-bottom-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_col_headings {</span></span>
-<span><span class="co">#&gt;   border-top-style: solid;</span></span>
-<span><span class="co">#&gt;   border-top-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-top-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   border-bottom-style: solid;</span></span>
-<span><span class="co">#&gt;   border-bottom-width: 2px;</span></span>
-<span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   border-left-style: none;</span></span>
-<span><span class="co">#&gt;   border-left-width: 1px;</span></span>
-<span><span class="co">#&gt;   border-left-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   border-right-style: none;</span></span>
-<span><span class="co">#&gt;   border-right-width: 1px;</span></span>
-<span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_col_heading {</span></span>
-<span><span class="co">#&gt;   color: #333333;</span></span>
-<span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
-<span><span class="co">#&gt;   font-size: 100%;</span></span>
-<span><span class="co">#&gt;   font-weight: normal;</span></span>
-<span><span class="co">#&gt;   text-transform: inherit;</span></span>
-<span><span class="co">#&gt;   border-left-style: none;</span></span>
-<span><span class="co">#&gt;   border-left-width: 1px;</span></span>
-<span><span class="co">#&gt;   border-left-color: #D3D3D3;</span></span>
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-<span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
-<span><span class="co">#&gt;   vertical-align: bottom;</span></span>
-<span><span class="co">#&gt;   padding-top: 5px;</span></span>
-<span><span class="co">#&gt;   padding-bottom: 6px;</span></span>
-<span><span class="co">#&gt;   padding-left: 5px;</span></span>
-<span><span class="co">#&gt;   padding-right: 5px;</span></span>
-<span><span class="co">#&gt;   overflow-x: hidden;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_column_spanner_outer {</span></span>
-<span><span class="co">#&gt;   color: #333333;</span></span>
-<span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
-<span><span class="co">#&gt;   font-size: 100%;</span></span>
-<span><span class="co">#&gt;   font-weight: normal;</span></span>
-<span><span class="co">#&gt;   text-transform: inherit;</span></span>
-<span><span class="co">#&gt;   padding-top: 0;</span></span>
-<span><span class="co">#&gt;   padding-bottom: 0;</span></span>
-<span><span class="co">#&gt;   padding-left: 4px;</span></span>
-<span><span class="co">#&gt;   padding-right: 4px;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #iuwzpsksfr .gt_column_spanner_outer:first-child {</span></span>
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-<span><span class="co">#&gt;   text-indent: 25px;</span></span>
-<span><span class="co">#&gt; }</span></span>
-<span><span class="co">#&gt; &lt;/style&gt;</span></span>
-<span><span class="co">#&gt;   &lt;table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false"&gt;</span></span>
-<span><span class="co">#&gt;   &lt;thead&gt;</span></span>
-<span><span class="co">#&gt;     </span></span>
-<span><span class="co">#&gt;     &lt;tr class="gt_col_headings"&gt;</span></span>
-<span><span class="co">#&gt;       &lt;th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="&amp;lt;strong&amp;gt;Characteristic&amp;lt;/strong&amp;gt;"&gt;&lt;strong&gt;Characteristic&lt;/strong&gt;&lt;/th&gt;</span></span>
-<span><span class="co">#&gt;       &lt;th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="&amp;lt;strong&amp;gt;Overall&amp;lt;/strong&amp;gt;, N = 200&amp;lt;span class=&amp;quot;gt_footnote_marks&amp;quot; style=&amp;quot;white-space:nowrap;font-style:italic;font-weight:normal;&amp;quot;&amp;gt;&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;&amp;lt;/span&amp;gt;"&gt;&lt;strong&gt;Overall&lt;/strong&gt;, N = 200&lt;span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;&lt;/th&gt;</span></span>
-<span><span class="co">#&gt;       &lt;th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="&amp;lt;strong&amp;gt;Active&amp;lt;/strong&amp;gt;, N = 79&amp;lt;span class=&amp;quot;gt_footnote_marks&amp;quot; style=&amp;quot;white-space:nowrap;font-style:italic;font-weight:normal;&amp;quot;&amp;gt;&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;&amp;lt;/span&amp;gt;"&gt;&lt;strong&gt;Active&lt;/strong&gt;, N = 79&lt;span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;&lt;/th&gt;</span></span>
-<span><span class="co">#&gt;       &lt;th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="&amp;lt;strong&amp;gt;Placebo&amp;lt;/strong&amp;gt;, N = 121&amp;lt;span class=&amp;quot;gt_footnote_marks&amp;quot; style=&amp;quot;white-space:nowrap;font-style:italic;font-weight:normal;&amp;quot;&amp;gt;&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;&amp;lt;/span&amp;gt;"&gt;&lt;strong&gt;Placebo&lt;/strong&gt;, N = 121&lt;span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;&lt;/th&gt;</span></span>
-<span><span class="co">#&gt;     &lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;   &lt;/thead&gt;</span></span>
-<span><span class="co">#&gt;   &lt;tbody class="gt_table_body"&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;&lt;td headers="label" class="gt_row gt_left"&gt;hypertension&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_0" class="gt_row gt_center"&gt;101 (50%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_1" class="gt_row gt_center"&gt;38 (48%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_2" class="gt_row gt_center"&gt;63 (52%)&lt;/td&gt;&lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;&lt;td headers="label" class="gt_row gt_left"&gt;diabetes&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_0" class="gt_row gt_center"&gt;23 (12%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_1" class="gt_row gt_center"&gt;9 (11%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_2" class="gt_row gt_center"&gt;14 (12%)&lt;/td&gt;&lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;&lt;td headers="label" class="gt_row gt_left"&gt;civil&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_0" class="gt_row gt_center"&gt;&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_1" class="gt_row gt_center"&gt;&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_2" class="gt_row gt_center"&gt;&lt;/td&gt;&lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;&lt;td headers="label" class="gt_row gt_left"&gt;    alone&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_0" class="gt_row gt_center"&gt;59 (30%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_1" class="gt_row gt_center"&gt;22 (28%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_2" class="gt_row gt_center"&gt;37 (31%)&lt;/td&gt;&lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;&lt;td headers="label" class="gt_row gt_left"&gt;    partner&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_0" class="gt_row gt_center"&gt;141 (70%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_1" class="gt_row gt_center"&gt;57 (72%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt; &lt;td headers="stat_2" class="gt_row gt_center"&gt;84 (69%)&lt;/td&gt;&lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;   &lt;/tbody&gt;</span></span>
-<span><span class="co">#&gt;   </span></span>
-<span><span class="co">#&gt;   &lt;tfoot class="gt_footnotes"&gt;</span></span>
-<span><span class="co">#&gt;     &lt;tr&gt;</span></span>
-<span><span class="co">#&gt;       &lt;td class="gt_footnote" colspan="4"&gt;&lt;span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; n (%)&lt;/td&gt;</span></span>
-<span><span class="co">#&gt;     &lt;/tr&gt;</span></span>
-<span><span class="co">#&gt;   &lt;/tfoot&gt;</span></span>
-<span><span class="co">#&gt; &lt;/table&gt;</span></span>
-<span><span class="co">#&gt; &lt;/div&gt;</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; $`Figure 1`</span></span></code></pre></div>
-<p><img src="toolbox_files/figure-html/generic_stroke-example-1.png" width="700"></p>
-<pre><code><span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; $`Figure 2`</span></span></code></pre>
-<p><img src="toolbox_files/figure-html/generic_stroke-example-2.png" width="700"></p>
-</div>
-<div class="section level4">
-<h4 id="index_plot">index_plot()<a class="anchor" aria-label="anchor" href="#index_plot"></a>
-</h4>
-<p>Used for plotting scores from a multi dimensional patient test.</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/index_plot.html">index_plot</a></span><span class="op">(</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="../reference/score.html">score</a></span><span class="op">[</span><span class="va">score</span><span class="op">$</span><span class="va">event</span> <span class="op">==</span> <span class="st">"A"</span>, <span class="op">]</span><span class="op">)</span></span></code></pre></div>
-<p><img src="toolbox_files/figure-html/index_plot-example-1.png" width="700"></p>
-</div>
-<div class="section level4">
-<h4 id="win_prob">win_prob()<a class="anchor" aria-label="anchor" href="#win_prob"></a>
-</h4>
-<p>The <code><a href="../reference/win_prob.html">win_prob()</a></code> is an implementation of the Tournament
-Method for calculating the probability of winning as suggested by <a href="https://doi.org/10.1161/STROKEAHA.121.037744" class="external-link">Zou et al 2022</a>.
-The authors has included a spreadsheet as supplementary materials. This
-function aims to mimic that functionality. The function also includes a
-<code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> extension for nice printing.</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../reference/win_prob.html">win_prob</a></span><span class="op">(</span></span>
-<span>  data <span class="op">=</span> <span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="../reference/talos.html">talos</a></span>,</span>
-<span>  response <span class="op">=</span> <span class="st">"mrs_6"</span>,</span>
-<span>  group <span class="op">=</span> <span class="st">"rtreat"</span>,</span>
-<span>  sample.size <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  print.tables <span class="op">=</span> <span class="cn">TRUE</span></span>
-<span><span class="op">)</span></span>
-<span><span class="co">#&gt;   Zou et al's winP (doi: 10.1161/STROKEAHA.121.037744) </span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; Probability of a random observation in Placebo group </span></span>
-<span><span class="co">#&gt;       will have a higher response score than a random</span></span>
-<span><span class="co">#&gt;       observation in Active group:</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt;         winP: 0.400 (0.612, 0.372)      p=0.0125</span></span>
-<span><span class="co">#&gt; --------------------------------------------</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; The numbers needed to treat (NNT) are: -9</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; --------------------------------------------</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt;  With Active/Placebo ratio = 1 and beta = 0.2</span></span>
-<span><span class="co">#&gt;               the sample size needed is: 238</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; --------------------------------------------</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; Results for the Active group:</span></span>
-<span><span class="co">#&gt;  |mrs_6 | Freq|  prop| overall_rank| rank| win_frac|</span></span>
-<span><span class="co">#&gt;      |:-----|----:|-----:|------------:|----:|--------:|</span></span>
-<span><span class="co">#&gt;      |0     |   14| 0.177|        175.0| 72.5|    0.847|</span></span>
-<span><span class="co">#&gt;      |1     |   29| 0.367|        113.5| 51.0|    0.517|</span></span>
-<span><span class="co">#&gt;      |2     |   22| 0.278|         49.0| 25.5|    0.194|</span></span>
-<span><span class="co">#&gt;      |3     |    9| 0.114|         15.0| 10.0|    0.041|</span></span>
-<span><span class="co">#&gt;      |4     |    3| 0.038|          7.0|  4.0|    0.025|</span></span>
-<span><span class="co">#&gt;      |6     |    2| 0.025|          2.5|  1.5|    0.008|</span></span>
-<span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; Results for the Placebo group:</span></span>
-<span><span class="co">#&gt;  |mrs_6 | Freq|  prop| overall_rank|  rank| win_frac|</span></span>
-<span><span class="co">#&gt;      |:-----|----:|-----:|------------:|-----:|--------:|</span></span>
-<span><span class="co">#&gt;      |0     |   37| 0.306|        175.0| 103.0|    0.911|</span></span>
-<span><span class="co">#&gt;      |1     |   43| 0.355|        113.5|  63.0|    0.639|</span></span>
-<span><span class="co">#&gt;      |2     |   35| 0.289|         49.0|  24.0|    0.316|</span></span>
-<span><span class="co">#&gt;      |3     |    2| 0.017|         15.0|   5.5|    0.120|</span></span>
-<span><span class="co">#&gt;      |4     |    2| 0.017|          7.0|   3.5|    0.044|</span></span>
-<span><span class="co">#&gt;      |6     |    2| 0.017|          2.5|   1.5|    0.013|</span></span></code></pre></div>
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-      <img src="../logo.png" class="logo" alt=""><h1>ds2dd</h1>
-            
-            <h4 data-toc-skip class="date">2023-06-07</h4>
-      
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/vignettes/ds2dd.Rmd" class="external-link"><code>vignettes/ds2dd.Rmd</code></a></small>
-      <div class="d-none name"><code>ds2dd.Rmd</code></div>
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-    
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://agdamsbo.github.io/stRoke/" class="external-link">stRoke</a></span><span class="op">)</span></span></code></pre></div>
-<div class="section level2">
-<h2 id="easy-data-set-to-data-base-workflow">Easy data set to data base workflow<a class="anchor" aria-label="anchor" href="#easy-data-set-to-data-base-workflow"></a>
-</h2>
-<p>This function can be used as a simple tool for creating at data base
-metadata file for REDCap (called a DataDictionary) based on a given data
-set file.</p>
-<div class="section level3">
-<h3 id="step-1---load-your-data-set">Step 1 - Load your data set<a class="anchor" aria-label="anchor" href="#step-1---load-your-data-set"></a>
-</h3>
-<p>Here we’ll use the sample TALOS dataset included with the
-package.</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"talos"</span><span class="op">)</span></span>
-<span><span class="va">ds</span> <span class="op">&lt;-</span> <span class="va">talos</span></span>
-<span><span class="co"># As the data set lacks an ID column, one is added</span></span>
-<span><span class="va">ds</span><span class="op">$</span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-</div>
-<div class="section level3">
-<h3 id="step-2---create-the-datadictionary">Step 2 - Create the DataDictionary<a class="anchor" aria-label="anchor" href="#step-2---create-the-datadictionary"></a>
-</h3>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">datadictionary</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ds2dd.html">ds2dd</a></span><span class="op">(</span><span class="va">ds</span>,record.id <span class="op">=</span> <span class="st">"id"</span>,include.column.names <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
-<p>Now additional specifications to the DataDictionary can be made
-manually, or it can be uploaded and modified manually in the graphical
-user interface on the web page.</p>
-<p>The function will transform column names to lower case and substitute
-spaces for underscores. The output is a list with the DataDictionary and
-a vector of new column names for the dataset to fit the meta data.</p>
-</div>
-<div class="section level3">
-<h3 id="step-3---meta-data-upload">Step 3 - Meta data upload<a class="anchor" aria-label="anchor" href="#step-3---meta-data-upload"></a>
-</h3>
-<p>Now the DataDictionary can be exported as a spreadsheet and uploaded
-or it can be uploaded using the <code>REDCapR</code> package (only
-projects with “Development” status).</p>
-<p>Use one of the two approaches below:</p>
-<div class="section level4">
-<h4 id="manual-upload">Manual upload<a class="anchor" aria-label="anchor" href="#manual-upload"></a>
-</h4>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/write.table.html" class="external-link">write.csv</a></span><span class="op">(</span><span class="va">datadictionary</span><span class="op">$</span><span class="va">DataDictionary</span>,<span class="st">"datadictionary.csv"</span><span class="op">)</span></span></code></pre></div>
-</div>
-<div class="section level4">
-<h4 id="upload-with-redcapr">Upload with <code>REDCapR</code><a class="anchor" aria-label="anchor" href="#upload-with-redcapr"></a>
-</h4>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_metadata_write.html" class="external-link">redcap_metadata_write</a></span><span class="op">(</span></span>
-<span>  <span class="va">datadictionary</span><span class="op">$</span><span class="va">DataDictionary</span>,</span>
-<span>  redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/keyring/man/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
-<span>  token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/keyring/man/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-<p>In the <a href="https://agdamsbo.github.io/redcap-r-handbook/" class="external-link">“REDCap R
-Handbook”</a> more is written on interfacing with REDCap in R using the
-<code><a href="https://r-lib.github.io/keyring/index.html" class="external-link">library(keyring)</a></code>to store credentials in <a href="https://agdamsbo.github.io/redcap-r-handbook/access.html#sec-getting-access" class="external-link">chapter
-1.1</a>.</p>
-</div>
-</div>
-<div class="section level3">
-<h3 id="step-4---data-upload">Step 4 - Data upload<a class="anchor" aria-label="anchor" href="#step-4---data-upload"></a>
-</h3>
-<p>The same two options are available for data upload as meta data
-upload: manual or through <code>REDCapR</code>.</p>
-<p>Only the latter is shown here.</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="co"># new column names are applied</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datadictionary</span><span class="op">$</span><span class="va">`Column names`</span></span>
-<span></span>
-<span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_write.html" class="external-link">redcap_write</a></span><span class="op">(</span></span>
-<span>  <span class="va">ds</span>,</span>
-<span>  redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/keyring/man/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
-<span>  token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/keyring/man/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
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-      <img src="" class="logo" alt=""><h1>Simple REDCap workflow</h1>
-            
-      
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/vignettes/redcap.Rmd" class="external-link"><code>vignettes/redcap.Rmd</code></a></small>
-      <div class="d-none name"><code>redcap.Rmd</code></div>
-    </div>
-
-    
-    
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://agdamsbo.github.io/stRoke/" class="external-link">stRoke</a></span><span class="op">)</span></span></code></pre></div>
-<div class="section level2">
-<h2 id="initial-note">Initial note<a class="anchor" aria-label="anchor" href="#initial-note"></a>
-</h2>
-<p>Please refer to the book <a href="https://agdamsbo.github.io/neuRo-group/" class="external-link">“neuRo-group”</a> for a
-more thorough guide on using R and REDCap together in data analysis, but
-also for notes and advices on how to build a REDCap database. Note, that
-this book is a work in progress with no goal of “completion”.</p>
-</div>
-<div class="section level2">
-<h2 id="working-with-data-from-redcap">Working with data from REDCap<a class="anchor" aria-label="anchor" href="#working-with-data-from-redcap"></a>
-</h2>
-<p><a href="https://www.project-redcap.org" class="external-link">REDCap</a> is an excellent
-tool for clinical data acquisition and storage. It is widely used world
-wide and is the standard tool for medical research data in Denmark.</p>
-<p>In the case of analysing data directly whole storing data in REDCap,
-the API functionality is very convenient and secure, as you are not
-storing (possibly) sensitive data permanently on your computer.</p>
-<p>When using the “events” or “repeated instruments” functionality of
-REDCap, the data storage format is a little confusing to work with, when
-being accustomed to tidy data.</p>
-<p>The <a href="https://ouhscbbmc.github.io/REDCapR/" class="external-link"><code>library(REDCapR)</code></a>
-provides a simple way of working with data, however, the package just
-exports data in standard format.</p>
-<div class="section level3">
-<h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
-</h3>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ouhscbbmc.github.io/REDCapR/" class="external-link">REDCapR</a></span><span class="op">)</span></span>
-<span><span class="co"># Returns the variables "record_id" and "age".</span></span>
-<span><span class="va">ds_some_vars</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a></span><span class="op">(</span></span>
-<span>  redcap_uri   <span class="op">=</span> <span class="st">"https://redcap.au.dk/api/"</span>,</span>
-<span>  <span class="co"># This is the address for projects at the AU-server</span></span>
-<span>  token        <span class="op">=</span> <span class="st">"YOUR_API_KEY_GOES_HERE"</span>,</span>
-<span>  fields       <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>, <span class="st">"age"</span><span class="op">)</span></span>
-<span><span class="op">)</span><span class="op">$</span><span class="va">data</span></span>
-<span></span>
-<span><span class="co"># Return only records with IDs of 1 and 4</span></span>
-<span><span class="va">ds_some_rows</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a></span><span class="op">(</span>redcap_uri   <span class="op">=</span> <span class="st">"https://redcap.au.dk/api/"</span>,</span>
-<span>                            <span class="co"># This is the address for projects at the AU-server</span></span>
-<span>                            token        <span class="op">=</span> <span class="st">"YOUR_API_KEY_GOES_HERE"</span>,</span>
-<span>                            records      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">data</span></span></code></pre></div>
-<p><em>more will be added</em></p>
-</div>
-</div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside>
-</div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
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-  <p></p>
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-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="logo.png" class="logo" alt=""><h1>Authors and Citation</h1>
-    </div>
-
-    <div class="section level2 citation">
-      <h2>Authors</h2>
-      
-      <ul class="list-unstyled"><li>
-          <p><strong>Andreas Gammelgaard Damsbo</strong>. Author, maintainer. <a href="https://orcid.org/0000-0002-7559-1154" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
-          </p>
-        </li>
-      </ul></div>
-
-    <div class="section level2 citation">
-      <h2 id="citation">Citation</h2>
-      <p><small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
-
-      <p>Damsbo A (2023).
-<em>stRoke: Clinical Stroke Research</em>.
-https://agdamsbo.github.io/stRoke/, https://github.com/agdamsbo/stRoke. 
-</p>
-      <pre>@Manual{,
-  title = {stRoke: Clinical Stroke Research},
-  author = {Andreas Gammelgaard Damsbo},
-  year = {2023},
-  note = {https://agdamsbo.github.io/stRoke/, https://github.com/agdamsbo/stRoke},
-}</pre>
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docs/index.html

@@ -1,180 +0,0 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="This is an R-toolbox of custom functions for convenient data management 
-    and analysis in clinical health research and teaching.
-    The package is mainly collected for personal use, but any use beyond that is encouraged.
-    This package has migrated functions from agdamsbo/daDoctoR, and new functions has been added.
-    Version follows months and year. See NEWS/Changelog for release notes.
-    This package includes sampled data from the TALOS trial (Kraglund et al (2018) &lt;doi:10.1161/STROKEAHA.117.020067&gt;).
-    The win_prob() function is based on work by Zou et al (2022) &lt;doi:10.1161/STROKEAHA.121.037744&gt;.
-    The age_calc() function is based on work by Becker (2020) &lt;doi:10.18637/jss.v093.i02&gt;.">
-<title>Clinical Stroke Research • stRoke</title>
-<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
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-<meta property="og:description" content="This is an R-toolbox of custom functions for convenient data management 
-    and analysis in clinical health research and teaching.
-    The package is mainly collected for personal use, but any use beyond that is encouraged.
-    This package has migrated functions from agdamsbo/daDoctoR, and new functions has been added.
-    Version follows months and year. See NEWS/Changelog for release notes.
-    This package includes sampled data from the TALOS trial (Kraglund et al (2018) &lt;doi:10.1161/STROKEAHA.117.020067&gt;).
-    The win_prob() function is based on work by Zou et al (2022) &lt;doi:10.1161/STROKEAHA.121.037744&gt;.
-    The age_calc() function is based on work by Becker (2020) &lt;doi:10.18637/jss.v093.i02&gt;.">
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-</nav><div class="container template-home">
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-  <main id="main" class="col-md-9">
-<div class="section level1">
-<div class="page-header">
-<img src="logo.png" class="logo" alt=""><h1 id="stroke-package-">stRoke package <a class="anchor" aria-label="anchor" href="#stroke-package-"></a>
-</h1>
-</div>
-<p>This is an R-toolbox of custom functions for convenient data management and analysis in clinical health research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from the agdamsbo/daDoctoR-package, and new functions has been added.</p>
-<div class="section level2">
-<h2 id="contribute">Contribute<a class="anchor" aria-label="anchor" href="#contribute"></a>
-</h2>
-<p>This package is <a href="https://github.com/agdamsbo/stRoke" class="external-link">shared on GitHub</a>, and you are very welcome to contribute by opening an issue or a pull request.</p>
-</div>
-</div>
-<div class="section level1">
-<h1 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
-</h1>
-<p>The package can be installed directly from CRAN:</p>
-<pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"stRoke"</span><span class="op">)</span></span></code></pre>
-<p>The latest version in development can be installed from GitHub:</p>
-<pre><code><span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"agdamsbo/stRoke"</span><span class="op">)</span></span></code></pre>
-</div>
-
-  </main><aside class="col-md-3"><div class="links">
-<h2 data-toc-skip>Links</h2>
-<ul class="list-unstyled">
-<li><a href="https://cloud.r-project.org/package=stRoke" class="external-link">View on CRAN</a></li>
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-      <small>Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
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-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.6.1" id="stroke-2361">stRoke 23.6.1<a class="anchor" aria-label="anchor" href="#stroke-2361"></a></h2>
-<div class="section level4">
-<h4 id="functions-23-6-1">Functions:<a class="anchor" aria-label="anchor" href="#functions-23-6-1"></a></h4>
-<ul><li>NEW: ‘color_plot()’ function implements the ‘contrast_text()’ and is very much inspired from ‘scales::show_col()’. Passes arguments to the internal ‘contrast_text()’. Tests and all. Took way longer than intended.</li>
-</ul></div>
-</div>
-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.4.1" id="stroke-2341">stRoke 23.4.1<a class="anchor" aria-label="anchor" href="#stroke-2341"></a></h2><p class="text-muted">CRAN release: 2023-04-13</p>
-<div class="section level4">
-<h4 id="functions-23-4-1">Functions:<a class="anchor" aria-label="anchor" href="#functions-23-4-1"></a></h4>
-<ul><li>NEW: ds2dd() creates a REDCap data dictionary based on a data set for easy upload. A new vignette will be provided for example use. A separate vignette has been added.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="notes-23-4-1">Notes:<a class="anchor" aria-label="anchor" href="#notes-23-4-1"></a></h4>
-<ul><li>With newer additions to the package, these functions clearly has their potential use also outside stroke research.</li>
-<li>A new vector with REDCap metadata headers has been added. Can be called with data(metadata_names).</li>
-</ul></div>
-</div>
-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.1.8" id="stroke-2318">stRoke 23.1.8<a class="anchor" aria-label="anchor" href="#stroke-2318"></a></h2>
-<div class="section level4">
-<h4 id="functions-23-1-8">Functions:<a class="anchor" aria-label="anchor" href="#functions-23-1-8"></a></h4>
-<ul><li>write_ical() is an easy to use implementation of the package <code><a href="https://rdrr.io/r/base/library.html" class="external-link">library(calendar)</a></code> for easy conversion of spreadsheets to ical object. Export an .ics file using <code><a href="https://rdrr.io/pkg/calendar/man/ic_write.html" class="external-link">calendar::ic_write()</a></code>.</li>
-<li>contrast_text() calculates the best contrast text color for a given background color. For use in graphics.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="notes-23-1-8">Notes:<a class="anchor" aria-label="anchor" href="#notes-23-1-8"></a></h4>
-<ul><li>This is the first update on CRAN.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="documentation-23-1-8">Documentation<a class="anchor" aria-label="anchor" href="#documentation-23-1-8"></a></h4>
-<ul><li>Badges, lots of badges</li>
-</ul></div>
-</div>
-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.1.7" id="stroke-2317">stRoke 23.1.7<a class="anchor" aria-label="anchor" href="#stroke-2317"></a></h2><p class="text-muted">CRAN release: 2023-01-24</p>
-<div class="section level4">
-<h4 id="notes-23-1-7">Notes:<a class="anchor" aria-label="anchor" href="#notes-23-1-7"></a></h4>
-<ul><li>This is the version first published on CRAN as of 24.jan.2023.</li>
-<li>This is also the version first published to zenodo.org, and with corresponding <a href="https://doi.org/10.5281/zenodo.7572023" class="external-link">doi: 10.5281/zenodo.7572023</a>.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="functions-23-1-7">Functions:<a class="anchor" aria-label="anchor" href="#functions-23-1-7"></a></h4>
-<ul><li>redcap_read_tables() has been removed from the package for now. Looking to add it back later as a minimal data acquisition tool.</li>
-</ul></div>
-</div>
-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.1.6" id="stroke-2316---failed-due-to-dependencies">stRoke 23.1.6 - failed due to dependencies<a class="anchor" aria-label="anchor" href="#stroke-2316---failed-due-to-dependencies"></a></h2>
-<div class="section level4">
-<h4 id="new-attempt-at-cran-submission-23-1-6">New attempt at CRAN submission<a class="anchor" aria-label="anchor" href="#new-attempt-at-cran-submission-23-1-6"></a></h4>
-</div>
-<div class="section level4">
-<h4 id="functions-23-1-6">Functions:<a class="anchor" aria-label="anchor" href="#functions-23-1-6"></a></h4>
-<ul><li>win_prop() added to implement the suggested methods in <a href="https://doi.org/10.1161/STROKEAHA.121.037744" class="external-link">DOI: 10.1161/STROKEAHA.121.037744</a>, as an implementation of “Tournament Methods” also found in <code><a href="https://rdrr.io/r/base/library.html" class="external-link">library(genodds)</a></code>. The function is based on the spreadsheet provided by the authors. A print.win_Prop is also added for printing.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="notes-23-1-6">Notes:<a class="anchor" aria-label="anchor" href="#notes-23-1-6"></a></h4>
-<ul><li>23.1.5 failed on CRAN due to gt_plot(). This function has been dropped. Find it as as_ggplot() elsewhere.</li>
-<li>agdamsbo/REDCapRITS added as “Additional_repositories”.</li>
-<li>Included references listed as authors.</li>
-</ul></div>
-</div>
-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="23.1.5" id="stroke-2315">stRoke 23.1.5<a class="anchor" aria-label="anchor" href="#stroke-2315"></a></h2>
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-<h4 id="release-on-cran---failed-23-1-5">RELEASE ON CRAN - failed<a class="anchor" aria-label="anchor" href="#release-on-cran---failed-23-1-5"></a></h4>
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-<h2 class="pkg-version" data-toc-text="0.23.1.4" id="stroke-02314">stRoke 0.23.1.4<a class="anchor" aria-label="anchor" href="#stroke-02314"></a></h2>
-<div class="section level4">
-<h4 id="functions-0-23-1-4">Functions:<a class="anchor" aria-label="anchor" href="#functions-0-23-1-4"></a></h4>
-<ul><li>plot_olr() has been deprecated and removed.</li>
-<li>ci_plot() functionality extended to include logistic model plotting.</li>
-<li>age_calc() use vapply() instead of sapply()</li>
-<li>gt_plot() function added to plot gt elements as ggplots. From <a href="https://github.com/MSKCC-Epi-Bio/bstfun" class="external-link">bstfun</a>. Not all done and satisfied with the layout with patchwork.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="documentation-0-23-1-4">Documentation<a class="anchor" aria-label="anchor" href="#documentation-0-23-1-4"></a></h4>
-<ul><li>Trying to complete all flags from goodpractice and inteRgrate</li>
-</ul></div>
-</div>
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-<h2 class="pkg-version" data-toc-text="0.23.1.3" id="stroke-02313">stRoke 0.23.1.3<a class="anchor" aria-label="anchor" href="#stroke-02313"></a></h2>
-<div class="section level4">
-<h4 id="functions-0-23-1-3">Functions:<a class="anchor" aria-label="anchor" href="#functions-0-23-1-3"></a></h4>
-<ul><li>files_filter() added. Simple function to get file names in path with specified filter.</li>
-<li>updated cpr_dob to give warnings if format is not recognised and return NAs.</li>
-<li>ci_plot() updated to actually handle binary factors. Uses glm(), not lm().</li>
-</ul></div>
-<div class="section level4">
-<h4 id="documentation-0-23-1-3">Documentation:<a class="anchor" aria-label="anchor" href="#documentation-0-23-1-3"></a></h4>
-<ul><li>test, test and tests to satisfy codecov and, of course, ensure higher quality</li>
-<li>changes to comply with goodpractices::gp()</li>
-</ul><p>…and probably some more.</p>
-</div>
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-    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.23.1.2" id="stroke-02312">stRoke 0.23.1.2<a class="anchor" aria-label="anchor" href="#stroke-02312"></a></h2>
-<div class="section level4">
-<h4 id="functions-0-23-1-2">Functions:<a class="anchor" aria-label="anchor" href="#functions-0-23-1-2"></a></h4>
-<ul><li>cpr_dob() now includes <code>format=</code>.</li>
-<li>Other minor updates.</li>
-</ul></div>
-<div class="section level4">
-<h4 id="documentation-0-23-1-2">Documentation:<a class="anchor" aria-label="anchor" href="#documentation-0-23-1-2"></a></h4>
-<ul><li>Two new vignettes</li>
-<li>Taking last steps in documenting before releasing on CRAN</li>
-</ul></div>
-<div class="section level4">
-<h4 id="other-0-23-1-2">Other:<a class="anchor" aria-label="anchor" href="#other-0-23-1-2"></a></h4>
-<ul><li>New hex logo</li>
-</ul></div>
-</div>
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-<h2 class="pkg-version" data-toc-text="0.23.1.1" id="stroke-02311">stRoke 0.23.1.1<a class="anchor" aria-label="anchor" href="#stroke-02311"></a></h2>
-<div class="section level4">
-<h4 id="functions-0-23-1-1">Functions:<a class="anchor" aria-label="anchor" href="#functions-0-23-1-1"></a></h4>
-<ul><li>age_calc() now also outputs a numeric vector for units=“days”, and not a character vector as difftime() would.</li>
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-<h4 id="documentation-0-23-1-1">Documentation:<a class="anchor" aria-label="anchor" href="#documentation-0-23-1-1"></a></h4>
-<ul><li>Added a <code>NEWS.md</code> file to track changes to the package.</li>
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docs/pkgdown.yml

@@ -1,8 +0,0 @@
-pandoc: 2.19.2
-pkgdown: 2.0.7
-pkgdown_sha: ~
-articles:
-  ds2dd: ds2dd.html
-  toolbox: toolbox.html
-last_built: 2023-06-07T12:03Z
-

docs/reference/age_calc.html

@@ -1,126 +0,0 @@
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-<div class="row">
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-      <img src="../logo.png" class="logo" alt=""><h1>Calculate age in years, months, or days</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/age_calc.R" class="external-link"><code>R/age_calc.R</code></a></small>
-      <div class="d-none name"><code>age_calc.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Calculate age in years, months, or days</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">age_calc</span><span class="op">(</span><span class="va">dob</span>, enddate <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>, units <span class="op">=</span> <span class="st">"years"</span>, precise <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p><a href="https://doi.org/10.18637/jss.v093.i02" class="external-link">doi:10.18637/jss.v093.i02</a></p>
-    </div>
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>dob</dt>
-<dd><p>Date of birth</p></dd>
-
-
-<dt>enddate</dt>
-<dd><p>End date for age calculation (default is Sys.Date())</p></dd>
-
-
-<dt>units</dt>
-<dd><p>Units for age calculation (default is "years").
-Can be c("days", "months", "years")</p></dd>
-
-
-<dt>precise</dt>
-<dd><p>Option to calculate age precisely (default is TRUE)</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>numeric vector length 1</p>
-    </div>
-    <div class="section level2">
-    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Becker, J.P. (2020). eeptools: An R Package for Teaching and Learning
-Ecology and Evolutionary Biology. Journal of Statistical Software,
-93(2), 1-27.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">trunc</a></span><span class="op">(</span><span class="fu">age_calc</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"1945-10-23"</span><span class="op">)</span>,<span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-09-30"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 72</span>
-<span class="r-in"><span></span></span>
-</code></pre></div>
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-    </nav></aside></div>
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docs/reference/ci_plot.html

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-Includes dichotomous or olr, depending on number of levels in "x".
-Title and axis labels can be added to the ggplot afterwards.'><title>Confidence interval plot with point estimate — ci_plot • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence interval plot with point estimate — ci_plot"><meta property="og:description" content='Horizontal forest plot of point estimate with confidence intervals.
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-      <img src="../logo.png" class="logo" alt=""><h1>Confidence interval plot with point estimate</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/ci_plot.R" class="external-link"><code>R/ci_plot.R</code></a></small>
-      <div class="d-none name"><code>ci_plot.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Horizontal forest plot of point estimate with confidence intervals.
-Includes dichotomous or olr, depending on number of levels in "x".
-Title and axis labels can be added to the ggplot afterwards.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ci_plot</span><span class="op">(</span></span>
-<span>  <span class="va">ds</span>,</span>
-<span>  x <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  y <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  dec <span class="op">=</span> <span class="fl">3</span>,</span>
-<span>  lbls <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  title <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  method <span class="op">=</span> <span class="st">"auto"</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ds</dt>
-<dd><p>main input, either data set or logistic model</p></dd>
-
-
-<dt>x</dt>
-<dd><p>text string of main exposure variable</p></dd>
-
-
-<dt>y</dt>
-<dd><p>text string of outcome variable</p></dd>
-
-
-<dt>vars</dt>
-<dd><p>variables for multivariate analysis.</p></dd>
-
-
-<dt>dec</dt>
-<dd><p>Decimals in labels</p></dd>
-
-
-<dt>lbls</dt>
-<dd><p>Labels for variable names</p></dd>
-
-
-<dt>title</dt>
-<dd><p>Plot title. Can be specified later.</p></dd>
-
-
-<dt>method</dt>
-<dd><p>Character vector. The method for the regression.
-Can be c("auto", "model").</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>ggplot element</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Auto plot</span></span></span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">talos</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">talos</span><span class="op">[</span>,<span class="st">"mrs_1"</span><span class="op">]</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">talos</span><span class="op">[</span>,<span class="st">"mrs_1"</span><span class="op">]</span>,ordered<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">ci_plot</span><span class="op">(</span>ds <span class="op">=</span> <span class="va">talos</span>, x <span class="op">=</span> <span class="st">"rtreat"</span>, y <span class="op">=</span> <span class="st">"mrs_1"</span>, </span></span>
-<span class="r-in"><span>vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hypertension"</span>,<span class="st">"diabetes"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Waiting for profiling to be done...</span>
-<span class="r-plt img"><img src="ci_plot-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span><span class="co">## Model plot</span></span></span>
-<span class="r-in"><span><span class="co"># iris$ord&lt;-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE)</span></span></span>
-<span class="r-in"><span><span class="co"># lm &lt;- MASS::polr(ord~., data=iris, Hess=TRUE, method="logistic")</span></span></span>
-<span class="r-in"><span><span class="co"># ci_plot(ds = lm, method="model")</span></span></span>
-</code></pre></div>
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-    </nav></aside></div>
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docs/reference/color_plot.html

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-contrast_text."><title>Plot color examples with contrasting text — color_plot • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot color examples with contrasting text — color_plot"><meta property="og:description" content="Plots color examples with contrasting text. Parameters are passed to
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-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Plot color examples with contrasting text</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/contrast_text.R" class="external-link"><code>R/contrast_text.R</code></a></small>
-      <div class="d-none name"><code>color_plot.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Plots color examples with contrasting text. Parameters are passed to
-contrast_text.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">color_plot</span><span class="op">(</span></span>
-<span>  <span class="va">colors</span>,</span>
-<span>  labels <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  borders <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  cex_label <span class="op">=</span> <span class="fl">1</span>,</span>
-<span>  ncol <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  <span class="va">...</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>colors</dt>
-<dd><p>Vector of colors to plot</p></dd>
-
-
-<dt>labels</dt>
-<dd><p>Show color names. Default is TRUE</p></dd>
-
-
-<dt>borders</dt>
-<dd><p>Border parameter for 'rect()' function. Default is NULL</p></dd>
-
-
-<dt>cex_label</dt>
-<dd><p>Label size. Default is 1.</p></dd>
-
-
-<dt>ncol</dt>
-<dd><p>Desired number of columns. Default is ceiling of square root to
-the length of 'colors' vector provided.</p></dd>
-
-
-<dt>...</dt>
-<dd><p>Parameters for the</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>base plot</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>bg<span class="op">=</span><span class="cn">NULL</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> named list()</span>
-<span class="r-in"><span><span class="va">colors</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/grDevices/colors.html" class="external-link">colors</a></span><span class="op">(</span><span class="op">)</span>,size <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">color_plot</span><span class="op">(</span><span class="va">colors</span>, method<span class="op">=</span><span class="st">"relative"</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="color_plot-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span></span></span>
-</code></pre></div>
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-    </nav></aside></div>
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-</div>
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docs/reference/contrast_text.html

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-background color."><title>Contrast Text Color — contrast_text • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Contrast Text Color — contrast_text"><meta property="og:description" content="Calculates the best contrast text color for a given
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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Contrast Text Color</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/contrast_text.R" class="external-link"><code>R/contrast_text.R</code></a></small>
-      <div class="d-none name"><code>contrast_text.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Calculates the best contrast text color for a given
-background color.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">contrast_text</span><span class="op">(</span></span>
-<span>  <span class="va">background</span>,</span>
-<span>  light_text <span class="op">=</span> <span class="st">"white"</span>,</span>
-<span>  dark_text <span class="op">=</span> <span class="st">"black"</span>,</span>
-<span>  threshold <span class="op">=</span> <span class="fl">0.5</span>,</span>
-<span>  method <span class="op">=</span> <span class="st">"perceived_2"</span>,</span>
-<span>  <span class="va">...</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>background</dt>
-<dd><p>A hex/named color value that represents the background.</p></dd>
-
-
-<dt>light_text</dt>
-<dd><p>A hex/named color value that represents the light text
-color.</p></dd>
-
-
-<dt>dark_text</dt>
-<dd><p>A hex/named color value that represents the dark text color.</p></dd>
-
-
-<dt>threshold</dt>
-<dd><p>A numeric value between 0 and 1 that is used to determine
-the luminance threshold of the background color for text color.</p></dd>
-
-
-<dt>method</dt>
-<dd><p>A character string that specifies the method for calculating
-the luminance. Three different methods are available:
-c("relative","perceived","perceived_2")</p></dd>
-
-
-<dt>...</dt>
-<dd><p>parameter overflow. Ignored.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A character string that contains the best contrast text color.</p>
-    </div>
-    <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>This function aids in deciding the font color to print on a given background.
-The function is based on the example provided by teppo:
-https://stackoverflow.com/a/66669838/21019325.
-The different methods provided are based on the methods outlined in the
-StackOverflow thread:
-https://stackoverflow.com/questions/596216/formula-to-determine-perceived-brightness-of-rgb-color</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">contrast_text</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#F2F2F2"</span>, <span class="st">"blue"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "black" "white"</span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="fu">contrast_text</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#F2F2F2"</span>, <span class="st">"blue"</span><span class="op">)</span>, method<span class="op">=</span><span class="st">"relative"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "black" "white"</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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-

docs/reference/cpr_check.html

@@ -1,118 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Checking validity of cpr number. Vectorised."><title>CPR check — cpr_check • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CPR check — cpr_check"><meta property="og:description" content="Checking validity of cpr number. Vectorised."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-    
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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>CPR check</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/cpr_tools.R" class="external-link"><code>R/cpr_tools.R</code></a></small>
-      <div class="d-none name"><code>cpr_check.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Checking validity of cpr number. Vectorised.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cpr_check</span><span class="op">(</span><span class="va">cpr</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cpr</dt>
-<dd><p>cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx.
-Also mixed formatting. Vector or data frame column.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Logical vector of cpr validity</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">fsd</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"2310450637"</span>, <span class="st">"010190-2000"</span>, <span class="st">"010115-4000"</span>,</span></span>
-<span class="r-in"><span><span class="st">"300450-1030"</span>,<span class="st">"010150-4021"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">cpr_check</span><span class="op">(</span><span class="st">"2310450637"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> OBS: as per 2007 not all valid CPR numbers apply to modulus 11 rule.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>     </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> See the vignette 'Toolbox'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
-<span class="r-in"><span><span class="fu">cpr_check</span><span class="op">(</span><span class="va">fsd</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> OBS: as per 2007 not all valid CPR numbers apply to modulus 11 rule.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>     </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> See the vignette 'Toolbox'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1]  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">cpr_check</span><span class="op">(</span><span class="va">fsd</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> OBS: as per 2007 not all valid CPR numbers apply to modulus 11 rule.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>     </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> See the vignette 'Toolbox'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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docs/reference/cpr_dob.html

@@ -1,111 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="For easy calculation. Does not handle cprs with letters (interim cpr)"><title>Extracting date of birth from CPR — cpr_dob • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extracting date of birth from CPR — cpr_dob"><meta property="og:description" content="For easy calculation. Does not handle cprs with letters (interim cpr)"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-      <img src="../logo.png" class="logo" alt=""><h1>Extracting date of birth from CPR</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/cpr_tools.R" class="external-link"><code>R/cpr_tools.R</code></a></small>
-      <div class="d-none name"><code>cpr_dob.Rd</code></div>
-    </div>
-
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-    <p>For easy calculation. Does not handle cprs with letters (interim cpr)</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cpr_dob</span><span class="op">(</span><span class="va">cpr</span>, format <span class="op">=</span> <span class="st">"%d-%m-%Y"</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
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-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cpr</dt>
-<dd><p>cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx.
-Also mixed formatting. Vector or data frame column.</p></dd>
-
-
-<dt>format</dt>
-<dd><p>character string of dob date format. Default is "%d-%m-%Y".</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>character vector</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">cpr_dob</span><span class="op">(</span><span class="st">"231045-0637"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "23-10-1945"</span>
-<span class="r-in"><span><span class="va">fsd</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"2310450637"</span>, <span class="st">"010190-2000"</span>, <span class="st">"010115-4000"</span>,</span></span>
-<span class="r-in"><span><span class="st">"300450-1030"</span>,<span class="st">"010150-4021"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">cpr_dob</span><span class="op">(</span><span class="va">fsd</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "23-10-1945" "01-01-1990" "01-01-2015" "30-04-1950" "01-01-1950"</span>
-</code></pre></div>
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docs/reference/cpr_female.html

@@ -1,119 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Just checking if last number of a string is equal or not."><title>Determine female sex from CPR — cpr_female • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determine female sex from CPR — cpr_female"><meta property="og:description" content="Just checking if last number of a string is equal or not."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-      <img src="../logo.png" class="logo" alt=""><h1>Determine female sex from CPR</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/cpr_tools.R" class="external-link"><code>R/cpr_tools.R</code></a></small>
-      <div class="d-none name"><code>cpr_female.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Just checking if last number of a string is equal or not.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cpr_female</span><span class="op">(</span><span class="va">cpr</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cpr</dt>
-<dd><p>Vector. cpr-numbers as ddmmyy"-."xxxx or ddmmyyxxxx.
-Also mixed formatting. Vector or data frame column.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Logical vector</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">cpr_female</span><span class="op">(</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="cprs.html">cprs</a></span><span class="op">[</span>,<span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121]  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157]  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
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docs/reference/cprs.html

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-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This is just a repeated sample of 8 synthesized cpr-numbers
-for testing purposes."><title>Data frame of 200 cpr numbers — cprs • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Data frame of 200 cpr numbers — cprs"><meta property="og:description" content="This is just a repeated sample of 8 synthesized cpr-numbers
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-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/cprs.R" class="external-link"><code>R/cprs.R</code></a></small>
-      <div class="d-none name"><code>cprs.Rd</code></div>
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-    <p>This is just a repeated sample of 8 synthesized cpr-numbers
-for testing purposes.</p>
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-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">cprs</span><span class="op">)</span></span></code></pre></div>
-    </div>
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-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 200 rows and 1 variable:</p><dl><dt>cpr</dt>
-<dd><p>Mixed format cpr-numbers, characters</p></dd>
-
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-</dl></div>
-    <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><a href="https://da.wikipedia.org/wiki/231045-0637" class="external-link">https://da.wikipedia.org/wiki/231045-0637</a></p></div>
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-      <img src="../logo.png" class="logo" alt=""><h1>Data set to data dictionary function</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/ds2dd.R" class="external-link"><code>R/ds2dd.R</code></a></small>
-      <div class="d-none name"><code>ds2dd.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Data set to data dictionary function</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ds2dd</span><span class="op">(</span></span>
-<span>  <span class="va">ds</span>,</span>
-<span>  record.id <span class="op">=</span> <span class="st">"record_id"</span>,</span>
-<span>  form.name <span class="op">=</span> <span class="st">"basis"</span>,</span>
-<span>  field.type <span class="op">=</span> <span class="st">"text"</span>,</span>
-<span>  field.label <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  include.column.names <span class="op">=</span> <span class="cn">FALSE</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ds</dt>
-<dd><p>data set</p></dd>
-
-
-<dt>record.id</dt>
-<dd><p>name or column number of id variable, moved to first row of
-data dictionary, character of integer. Default is "record_id".</p></dd>
-
-
-<dt>form.name</dt>
-<dd><p>vector of form names, character string, length 1 or length
-equal to number of variables. Default is "basis".</p></dd>
-
-
-<dt>field.type</dt>
-<dd><p>vector of field types, character string, length 1 or length
-equal to number of variables. Default is "text.</p></dd>
-
-
-<dt>field.label</dt>
-<dd><p>vector of form names, character string, length 1 or length
-equal to number of variables. Default is NULL and is then identical to field
-names.</p></dd>
-
-
-<dt>include.column.names</dt>
-<dd><p>Flag to give detailed output including new
-column names for original data set for upload.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>data.frame or list of data.frame and vector</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">talos</span><span class="op">$</span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">talos</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">ds2dd</span><span class="op">(</span><span class="va">talos</span>, record.id<span class="op">=</span><span class="st">"id"</span>,include.column.names<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>     field_name form_name section_header field_type  field_label</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1           id     basis             NA       text           id</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2       rtreat     basis             NA       text       rtreat</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3        mrs_1     basis             NA       text        mrs_1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4        mrs_6     basis             NA       text        mrs_6</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5 hypertension     basis             NA       text hypertension</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6     diabetes     basis             NA       text     diabetes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7        civil     basis             NA       text        civil</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   select_choices_or_calculations field_note</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7                             NA         NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   text_validation_type_or_show_slider_number text_validation_min</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7                                         NA                  NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   text_validation_max identifier branching_logic required_field</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7                  NA         NA              NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   custom_alignment question_number matrix_group_name matrix_ranking</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7               NA              NA                NA             NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   field_annotation</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6               NA</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7               NA</span>
-</code></pre></div>
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-      <img src="../logo.png" class="logo" alt=""><h1>Filter files in a folder</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/files_filter.R" class="external-link"><code>R/files_filter.R</code></a></small>
-      <div class="d-none name"><code>files_filter.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>This function filters files in a folder based on the
-provided filter.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">files_filter</span><span class="op">(</span><span class="va">folder.path</span>, <span class="va">filter.by</span>, full.names <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
-    </div>
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-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>folder.path</dt>
-<dd><p>character. Path of the folder to be filtered</p></dd>
-
-
-<dt>filter.by</dt>
-<dd><p>character. Filter to be applied on the files</p></dd>
-
-
-<dt>full.names</dt>
-<dd><p>logical. Whether to return full file names or not</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>character vector. Filtered files</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Gives path to files/folders with "tests" in the name in the </span></span></span>
-<span class="r-in"><span><span class="co"># working directory</span></span></span>
-<span class="r-in"><span><span class="fu">files_filter</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/getwd.html" class="external-link">getwd</a></span><span class="op">(</span><span class="op">)</span>,<span class="st">"tests"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</span>
-</code></pre></div>
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docs/reference/generic_stroke.html

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-Please just use this function for illustration purposes.
-To dos: modify grottaBar and include as own function."><title>Generic stroke study outcome — generic_stroke • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generic stroke study outcome — generic_stroke"><meta property="og:description" content="Includes table 1, grotta bars and ordinal logistic regression plot.
-Please just use this function for illustration purposes.
-To dos: modify grottaBar and include as own function."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <img src="../logo.png" class="logo" alt=""><h1>Generic stroke study outcome</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/generic_stroke.R" class="external-link"><code>R/generic_stroke.R</code></a></small>
-      <div class="d-none name"><code>generic_stroke.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Includes table 1, grotta bars and ordinal logistic regression plot.
-Please just use this function for illustration purposes.
-To dos: modify grottaBar and include as own function.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">generic_stroke</span><span class="op">(</span><span class="va">df</span>, <span class="va">group</span>, <span class="va">score</span>, strata <span class="op">=</span> <span class="cn">NULL</span>, variables <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>df</dt>
-<dd><p>Data set as data frame</p></dd>
-
-
-<dt>group</dt>
-<dd><p>Variable to group by</p></dd>
-
-
-<dt>score</dt>
-<dd><p>Outcome measure variable</p></dd>
-
-
-<dt>strata</dt>
-<dd><p>Optional variable to stratify by</p></dd>
-
-
-<dt>variables</dt>
-<dd><p>String of variable names to include in adjusted OLR-analysis</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Returns list with three elements</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># generic_stroke(df = stRoke::talos, group = "rtreat", score = "mrs_6", </span></span></span>
-<span class="r-in"><span><span class="co"># variables = c("hypertension","diabetes","civil"))</span></span></span>
-<span class="r-in"></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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-

docs/reference/gt_plot.html

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-      <img src="" class="logo" alt=""><h1>Plot a gt or gtsummary table as ggplot object</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/gt_plot.R" class="external-link"><code>R/gt_plot.R</code></a></small>
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-    <p>Relying on <code><a href="https://docs.ropensci.org/magick/" class="external-link">library(magick)</a></code> and <code><a href="https://github.com/rstudio/webshot2" class="external-link">library(webshot2)</a></code></p>
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-<dd><p>A 'gt' or 'gtsummary' table</p></dd>
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-        <dd>Plot multidimensional cognitive test scores</dd>
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-        <dd>Helper function for labels in gtsummary</dd>
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-        <dd>Vector of REDCap metadata headers</dd>
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-          <code><a href="print.win_Prob.html">print(<i>&lt;win_Prob&gt;</i>)</a></code> 
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-        </dt>
-        <dd>Calculates the probability of winning</dd>
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-Includes option to facet."><title>Plot multidimensional cognitive test scores — index_plot • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot multidimensional cognitive test scores — index_plot"><meta property="og:description" content="Plot index scores from five dimensional cognitive testing.
-Includes option to facet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-      <img src="../logo.png" class="logo" alt=""><h1>Plot multidimensional cognitive test scores</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/index_plot.R" class="external-link"><code>R/index_plot.R</code></a></small>
-      <div class="d-none name"><code>index_plot.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Plot index scores from five dimensional cognitive testing.
-Includes option to facet.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">index_plot</span><span class="op">(</span></span>
-<span>  <span class="va">ds</span>,</span>
-<span>  id <span class="op">=</span> <span class="st">"id"</span>,</span>
-<span>  sub_plot <span class="op">=</span> <span class="st">"_is"</span>,</span>
-<span>  scores <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"_is"</span>, <span class="st">"_lo"</span>, <span class="st">"_up"</span>, <span class="st">"_per"</span><span class="op">)</span>,</span>
-<span>  dom_names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"immediate"</span>, <span class="st">"visuospatial"</span>, <span class="st">"verbal"</span>, <span class="st">"attention"</span>, <span class="st">"delayed"</span>, <span class="st">"total"</span><span class="op">)</span>,</span>
-<span>  facet.by <span class="op">=</span> <span class="cn">NULL</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ds</dt>
-<dd><p>complete data frame</p></dd>
-
-
-<dt>id</dt>
-<dd><p>colname of id column. Base for colouring</p></dd>
-
-
-<dt>sub_plot</dt>
-<dd><p>main outcome scores variable to plot</p></dd>
-
-
-<dt>scores</dt>
-<dd><p>variables to subset for plotting. Has to follow standard
-naming (is to be changed)</p></dd>
-
-
-<dt>dom_names</dt>
-<dd><p>domain names for axis naming</p></dd>
-
-
-<dt>facet.by</dt>
-<dd><p>variable to base facet_grid on</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>ggplot element</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">index_plot</span><span class="op">(</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="score.html">score</a></span><span class="op">[</span><span class="va">score</span><span class="op">$</span><span class="va">event</span><span class="op">==</span><span class="st">"A"</span>,<span class="op">]</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="index_plot-1.png" alt="" width="700" height="433"></span>
-</code></pre></div>
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docs/reference/label_select.html

@@ -1,132 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Function to select labels from list of label pairs (format: age~"Age").
-Alternative is to use attributes, eg from library(Hmisc).'><title>Helper function for labels in gtsummary — label_select • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for labels in gtsummary — label_select"><meta property="og:description" content='Function to select labels from list of label pairs (format: age~"Age").
-Alternative is to use attributes, eg from library(Hmisc).'><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function for labels in gtsummary</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/label_select.R" class="external-link"><code>R/label_select.R</code></a></small>
-      <div class="d-none name"><code>label_select.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Function to select labels from list of label pairs (format: <code>age~"Age"</code>).
-Alternative is to use attributes, eg from <code><a href="https://hbiostat.org/R/Hmisc/" class="external-link">library(Hmisc)</a></code>.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">label_select</span><span class="op">(</span><span class="va">lst</span>, <span class="va">vec</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>lst</dt>
-<dd><p>List of variables and labels (format: <code>age~"Age"</code>)</p></dd>
-
-
-<dt>vec</dt>
-<dd><p>Vector of variables to be subset from the list</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List of labels ordered like vec, formatted like lst</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">vars</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hypertension"</span>, <span class="st">"diabetes"</span>, <span class="st">"mrs_1"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">labels_all</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">rtreat</span><span class="op">~</span><span class="st">"Trial treatment"</span>,</span></span>
-<span class="r-in"><span><span class="va">civil</span><span class="op">~</span><span class="st">"Cohabitation"</span>,</span></span>
-<span class="r-in"><span><span class="va">diabetes</span><span class="op">~</span><span class="st">"Known diabetes"</span>, </span></span>
-<span class="r-in"><span><span class="va">hypertension</span><span class="op">~</span><span class="st">"Known hypertension"</span>, </span></span>
-<span class="r-in"><span><span class="va">mrs_1</span><span class="op">~</span><span class="st">"One month mRS"</span>, </span></span>
-<span class="r-in"><span><span class="va">mrs_6</span><span class="op">~</span><span class="st">"Six months mRS"</span>, </span></span>
-<span class="r-in"><span><span class="st">'[Intercept]'</span><span class="op">~</span><span class="st">"Intercept"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">label_select</span><span class="op">(</span><span class="va">labels_all</span>,<span class="va">vars</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> hypertension ~ "Known hypertension"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7f7d3e72d958&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> diabetes ~ "Known diabetes"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7f7d3e72d958&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [[3]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mrs_1 ~ "One month mRS"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7f7d3e72d958&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co">## With gtsummary::tbl_summary()</span></span></span>
-<span class="r-in"><span><span class="co">#stRoke::talos[vars] |&gt; </span></span></span>
-<span class="r-in"><span><span class="co">#gtsummary::tbl_summary(label = label_select(labels_all,vars))</span></span></span>
-</code></pre></div>
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docs/reference/metadata_names.html

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docs/reference/plot_olr.html

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-      <img src="" class="logo" alt=""><h1>Forest plot from ordinal logistic regression.</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/plot_olr.R" class="external-link"><code>R/plot_olr.R</code></a></small>
-      <div class="d-none name"><code>plot_olr.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_olr</span><span class="op">(</span></span>
-<span>  <span class="va">x</span>,</span>
-<span>  title <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  dec <span class="op">=</span> <span class="fl">3</span>,</span>
-<span>  lbls <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  hori <span class="op">=</span> <span class="st">"OR (95 % CI)"</span>,</span>
-<span>  vert <span class="op">=</span> <span class="st">"Variables"</span>,</span>
-<span>  short <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  input <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"model"</span>, <span class="st">"df"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>input data.</p></dd>
-
-
-<dt>title</dt>
-<dd><p>plot title</p></dd>
-
-
-<dt>dec</dt>
-<dd><p>decimals for labels</p></dd>
-
-
-<dt>lbls</dt>
-<dd><p>labels for variable names. Careful, as the right order is not checked automatically!</p></dd>
-
-
-<dt>hori</dt>
-<dd><p>labels the horizontal axis (this i the y axis as the plot is rotated)</p></dd>
-
-
-<dt>vert</dt>
-<dd><p>labels the horizontal axis (this i the x axis as the plot is rotated)</p></dd>
-
-
-<dt>short</dt>
-<dd><p>flag to half number of ticks on horizontal axis.</p></dd>
-
-
-<dt>input</dt>
-<dd><p>can be either "model", which is a olr model (polr()), or "df", which is a data frame with three columns for OR, lower CI and upper CI.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>gg object</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">iris</span><span class="op">$</span><span class="va">ord</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>,size<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">iris</span><span class="op">)</span>,replace<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span>,ordered<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">lm</span> <span class="op">&lt;-</span> <span class="fu">MASS</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/MASS/man/polr.html" class="external-link">polr</a></span><span class="op">(</span><span class="va">ord</span><span class="op">~</span><span class="va">.</span>, data<span class="op">=</span><span class="va">iris</span>, Hess<span class="op">=</span><span class="cn">TRUE</span>, method<span class="op">=</span><span class="st">"logistic"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">plot_olr</span><span class="op">(</span><span class="va">lm</span>, input<span class="op">=</span><span class="st">"model"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Waiting for profiling to be done...</span>
-<span class="r-plt img"><img src="plot_olr-1.png" alt="" width="700" height="433"></span>
-</code></pre></div>
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docs/reference/plot_ord_odds.html

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-      <img src="" class="logo" alt=""><h1>Forrest plot from ordinal logistic regression.</h1>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_ord_odds</span><span class="op">(</span></span>
-<span>  <span class="va">x</span>,</span>
-<span>  title <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  dec <span class="op">=</span> <span class="fl">3</span>,</span>
-<span>  lbls <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  hori <span class="op">=</span> <span class="st">"OR (95 % CI)"</span>,</span>
-<span>  vert <span class="op">=</span> <span class="st">"Variables"</span>,</span>
-<span>  short <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  input <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"model"</span>, <span class="st">"df"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
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-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>input data.</p></dd>
-
-
-<dt>title</dt>
-<dd><p>plot title</p></dd>
-
-
-<dt>dec</dt>
-<dd><p>decimals for labels</p></dd>
-
-
-<dt>lbls</dt>
-<dd><p>labels for variable names. Carefull, as the right order is not checked automatically!</p></dd>
-
-
-<dt>hori</dt>
-<dd><p>labels the horizontal axis (this i the y axis as the plot is rotated)</p></dd>
-
-
-<dt>vert</dt>
-<dd><p>labels the horizontal axis (this i the x axis as the plot is rotated)</p></dd>
-
-
-<dt>short</dt>
-<dd><p>flag to half number of ticks on horizontal axis.</p></dd>
-
-
-<dt>input</dt>
-<dd><p>can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI.</p></dd>
-
-</dl></div>
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docs/reference/print.win_Prob.html

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-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/win_prob.R" class="external-link"><code>R/win_prob.R</code></a></small>
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-<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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-    <dl><dt>x</dt>
-<dd><p>win_prob results.</p></dd>
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-
-<dt>...</dt>
-<dd><p>ignored for now</p></dd>
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docs/reference/quantile_cut.html

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-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/ds2dd.html">ds2dd</a>
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-</li>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
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-  <a class="external-link nav-link" href="https://github.com/agdamsbo/stRoke/" aria-label="github">
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-     
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-</li>
-      </ul></div>
-
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-</nav><div class="container template-reference-topic">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Easy function for splitting numeric variable in quantiles</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/quantile_cut.R" class="external-link"><code>R/quantile_cut.R</code></a></small>
-      <div class="d-none name"><code>quantile_cut.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Using base/stats functions cut() and quantile().</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">quantile_cut</span><span class="op">(</span></span>
-<span>  <span class="va">x</span>,</span>
-<span>  <span class="va">groups</span>,</span>
-<span>  y <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  na.rm <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  group.names <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  ordered.f <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  inc.outs <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  detail.list <span class="op">=</span> <span class="cn">FALSE</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>Variable to cut.</p></dd>
-
-
-<dt>groups</dt>
-<dd><p>Number of groups.</p></dd>
-
-
-<dt>y</dt>
-<dd><p>alternative vector to draw quantile cuts from. Limits has
-to be within x. Default is NULL.</p></dd>
-
-
-<dt>na.rm</dt>
-<dd><p>Remove NA's. Default is TRUE.</p></dd>
-
-
-<dt>group.names</dt>
-<dd><p>Names of groups to split to. Default is NULL,
-giving intervals as names.</p></dd>
-
-
-<dt>ordered.f</dt>
-<dd><p>Set resulting vector as ordered. Default is FALSE.</p></dd>
-
-
-<dt>inc.outs</dt>
-<dd><p>Flag to include min(x) and max(x)
-as borders in case of y!=NULL.</p></dd>
-
-
-<dt>detail.list</dt>
-<dd><p>flag to include details or not</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>vector or list with vector and details (length 2)</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">aa</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">1000</span>,<span class="fl">2000</span>,replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fl">1</span><span class="op">:</span><span class="fl">450</span></span></span>
-<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fl">6</span><span class="op">:</span><span class="fl">750</span></span></span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu">quantile_cut</span><span class="op">(</span><span class="va">aa</span>,groups<span class="op">=</span><span class="fl">4</span>,detail.list<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span> <span class="co">## Cuts quartiles</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>     [1,250]   (250,506]   (506,747] (747,1e+03] </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         501         500         501         498 </span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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-

docs/reference/read_redcap_data.html

@@ -1,122 +0,0 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split including some clean-up.
-Handles"><title>Download REDCap data — read_redcap_data • stRoke</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Download REDCap data — read_redcap_data"><meta property="og:description" content="Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split including some clean-up.
-Handles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
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-    
-    <a class="navbar-brand me-2" href="../index.html">stRoke</a>
-
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-
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-      <img src="" class="logo" alt=""><h1>Download REDCap data</h1>
-      
-      <div class="d-none name"><code>read_redcap_data.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split including some clean-up.
-Handles</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_redcap_data</span><span class="op">(</span></span>
-<span>  <span class="va">uri</span>,</span>
-<span>  <span class="va">token</span>,</span>
-<span>  records <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  fields <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  events <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  forms <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  generics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>, <span class="st">"redcap_event_name"</span>, <span class="st">"redcap_repeat_instrument"</span>,</span>
-<span>    <span class="st">"redcap_repeat_instance"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>uri</dt>
-<dd><p>REDCap database uri</p></dd>
-
-
-<dt>token</dt>
-<dd><p>API token</p></dd>
-
-
-<dt>records</dt>
-<dd><p>records to download</p></dd>
-
-
-<dt>fields</dt>
-<dd><p>fields to download</p></dd>
-
-
-<dt>events</dt>
-<dd><p>events to download</p></dd>
-
-
-<dt>forms</dt>
-<dd><p>forms to download</p></dd>
-
-
-<dt>generics</dt>
-<dd><p>vector of auto-generated generic variable names to ignore when discarding empty rows</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>list of instruments</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Examples will be provided later</span></span></span>
-<span class="r-in"></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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-
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-  </body></html>
-

docs/reference/read_redcap_tables.html

@@ -1,142 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
-including some clean-up. Works with longitudinal projects with repeating
-instruments."><title>Download REDCap data — read_redcap_tables • stRoke</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Download REDCap data — read_redcap_tables"><meta property="og:description" content="Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
-including some clean-up. Works with longitudinal projects with repeating
-instruments."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
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-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">23.1.6</small>
-
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-    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-      <img src="" class="logo" alt=""><h1>Download REDCap data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/read_redcap_tables.R" class="external-link"><code>R/read_redcap_tables.R</code></a></small>
-      <div class="d-none name"><code>read_redcap_tables.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
-including some clean-up. Works with longitudinal projects with repeating
-instruments.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_redcap_tables</span><span class="op">(</span></span>
-<span>  <span class="va">uri</span>,</span>
-<span>  <span class="va">token</span>,</span>
-<span>  records <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  fields <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  events <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  forms <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  generics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>, <span class="st">"redcap_event_name"</span>, <span class="st">"redcap_repeat_instrument"</span>,</span>
-<span>    <span class="st">"redcap_repeat_instance"</span><span class="op">)</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>uri</dt>
-<dd><p>REDCap database uri</p></dd>
-
-
-<dt>token</dt>
-<dd><p>API token</p></dd>
-
-
-<dt>records</dt>
-<dd><p>records to download</p></dd>
-
-
-<dt>fields</dt>
-<dd><p>fields to download</p></dd>
-
-
-<dt>events</dt>
-<dd><p>events to download</p></dd>
-
-
-<dt>forms</dt>
-<dd><p>forms to download</p></dd>
-
-
-<dt>generics</dt>
-<dd><p>vector of auto-generated generic variable names to
-ignore when discarding empty rows</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>list of instruments</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Examples will be provided later</span></span></span>
-<span class="r-in"></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
-
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-
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-  
-
-  </body></html>
-

docs/reference/score.html

@@ -1,169 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains non-identifiable organic trial data from a
-five-dimensional cognitive test."><title>Data frame with sample data of cognitive testing score — score • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Data frame with sample data of cognitive testing score — score"><meta property="og:description" content="Contains non-identifiable organic trial data from a
-five-dimensional cognitive test."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
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-    <a class="navbar-brand me-2" href="../index.html">stRoke</a>
-
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-
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-</li>
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-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-  </div>
-</li>
-<li class="nav-item">
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-</li>
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-</nav><div class="container template-reference-topic">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Data frame with sample data of cognitive testing score</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/score.R" class="external-link"><code>R/score.R</code></a></small>
-      <div class="d-none name"><code>score.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Contains non-identifiable organic trial data from a
-five-dimensional cognitive test.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">score</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 20 rows and 26 variables:</p><dl><dt>id</dt>
-<dd><p>id</p></dd>
-
-<dt>event</dt>
-<dd><p>event</p></dd>
-
-<dt>a_is</dt>
-<dd><p>domain a index score</p></dd>
-
-<dt>b_is</dt>
-<dd><p>domain b index score</p></dd>
-
-<dt>c_is</dt>
-<dd><p>domain c index score</p></dd>
-
-<dt>d_is</dt>
-<dd><p>domain d index score</p></dd>
-
-<dt>e_is</dt>
-<dd><p>domain e index score</p></dd>
-
-<dt>i_is</dt>
-<dd><p>total index score</p></dd>
-
-<dt>a_lo</dt>
-<dd><p>domain a lower ci</p></dd>
-
-<dt>b_lo</dt>
-<dd><p>domain b lower ci</p></dd>
-
-<dt>c_lo</dt>
-<dd><p>domain c lower ci</p></dd>
-
-<dt>d_lo</dt>
-<dd><p>domain d lower ci</p></dd>
-
-<dt>e_lo</dt>
-<dd><p>domain e lower ci</p></dd>
-
-<dt>i_lo</dt>
-<dd><p>total lower ci</p></dd>
-
-<dt>a_up</dt>
-<dd><p>domain a upper ci</p></dd>
-
-<dt>b_up</dt>
-<dd><p>domain b upper ci</p></dd>
-
-<dt>c_up</dt>
-<dd><p>domain c upper ci</p></dd>
-
-<dt>d_up</dt>
-<dd><p>domain d upper ci</p></dd>
-
-<dt>e_up</dt>
-<dd><p>domain e upper ci</p></dd>
-
-<dt>i_up</dt>
-<dd><p>total upper ci</p></dd>
-
-<dt>a_per</dt>
-<dd><p>domain a percentile</p></dd>
-
-<dt>b_per</dt>
-<dd><p>domain b percentile</p></dd>
-
-<dt>c_per</dt>
-<dd><p>domain c percentile</p></dd>
-
-<dt>d_per</dt>
-<dd><p>domain d percentile</p></dd>
-
-<dt>e_per</dt>
-<dd><p>domain e percentile</p></dd>
-
-<dt>i_per</dt>
-<dd><p>total percentile</p></dd>
-
-
-</dl></div>
-
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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-  
-
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-

docs/reference/source_lines.html

@@ -1,121 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sources specific lines from a file"><title>Source Lines from a File — source_lines • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Source Lines from a File — source_lines"><meta property="og:description" content="Sources specific lines from a file"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
-
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="../index.html">stRoke</a>
-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">23.6.1</small>
-
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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Source Lines from a File</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/source_lines.R" class="external-link"><code>R/source_lines.R</code></a></small>
-      <div class="d-none name"><code>source_lines.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Sources specific lines from a file</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">source_lines</span><span class="op">(</span><span class="va">file</span>, <span class="va">lines</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>file</dt>
-<dd><p>A character string giving the path to the file to be sourced.</p></dd>
-
-
-<dt>lines</dt>
-<dd><p>A numeric vector of line numbers to be sourced.</p></dd>
-
-
-<dt>...</dt>
-<dd><p>Additional arguments to be passed to <code><a href="https://rdrr.io/r/base/source.html" class="external-link">source</a></code>.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The result of <code><a href="https://rdrr.io/r/base/source.html" class="external-link">source</a></code>.</p>
-    </div>
-    <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p>This function is borrowed from a
-<a href="https://gist.github.com/christophergandrud/1eb4e095974204b12af9" class="external-link">gist</a>
-by christophergandrud.</p></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">test_file</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempfile</a></span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".R"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/writeLines.html" class="external-link">writeLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"# Line 1"</span>, <span class="st">"2+2"</span>, <span class="st">"# Line 3"</span><span class="op">)</span>, <span class="va">test_file</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">source_lines</span><span class="op">(</span><span class="va">test_file</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, echo<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &gt; 2 + 2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4</span>
-<span class="r-in"><span></span></span>
-</code></pre></div>
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docs/reference/stRoke-package.html

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-This is an R-toolbox of custom functions for convenient data management and analysis in clinical health research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) doi:10.1161/STROKEAHA.117.020067
-). The win_prob() function is based on work by Zou et al (2022) doi:10.1161/STROKEAHA.121.037744
-. The age_calc() function is based on work by Becker (2020) doi:10.18637/jss.v093.i02
-."><title>stRoke: Clinical Stroke Research — stRoke-package • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="stRoke: Clinical Stroke Research — stRoke-package"><meta property="og:description" content="
-This is an R-toolbox of custom functions for convenient data management and analysis in clinical health research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) doi:10.1161/STROKEAHA.117.020067
-). The win_prob() function is based on work by Zou et al (2022) doi:10.1161/STROKEAHA.121.037744
-. The age_calc() function is based on work by Becker (2020) doi:10.18637/jss.v093.i02
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-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/stRoke-package.R" class="external-link"><code>R/stRoke-package.R</code></a></small>
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-    <div class="ref-description section level2">
-    <p></p>
-<p>This is an R-toolbox of custom functions for convenient data management and analysis in clinical health research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) <a href="https://doi.org/10.1161/STROKEAHA.117.020067" class="external-link">doi:10.1161/STROKEAHA.117.020067</a>
-). The win_prob() function is based on work by Zou et al (2022) <a href="https://doi.org/10.1161/STROKEAHA.121.037744" class="external-link">doi:10.1161/STROKEAHA.121.037744</a>
-. The age_calc() function is based on work by Becker (2020) <a href="https://doi.org/10.18637/jss.v093.i02" class="external-link">doi:10.18637/jss.v093.i02</a>
-.</p>
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-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://agdamsbo.github.io/stRoke/" class="external-link">https://agdamsbo.github.io/stRoke/</a></p></li>
-<li><p><a href="https://github.com/agdamsbo/stRoke" class="external-link">https://github.com/agdamsbo/stRoke</a></p></li>
-<li><p>Report bugs at <a href="https://github.com/agdamsbo/stRoke/issues" class="external-link">https://github.com/agdamsbo/stRoke/issues</a></p></li>
-</ul></div>
-    </div>
-    <div class="section level2">
-    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
-    <p><strong>Maintainer</strong>: Andreas Gammelgaard Damsbo <a href="mailto:agdamsbo@clin.au.dk">agdamsbo@clin.au.dk</a> (<a href="https://orcid.org/0000-0002-7559-1154" class="external-link">ORCID</a>)</p>
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docs/reference/talos.html

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-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/talos.R" class="external-link"><code>R/talos.R</code></a></small>
-      <div class="d-none name"><code>talos.Rd</code></div>
-    </div>
-
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-    <p>Contains of non-identifiable subset of data from the TALOS trial.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">talos</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 200 rows and 6 variables:</p><dl><dt>rtreat</dt>
-<dd><p>Randomisation</p></dd>
-
-<dt>mrs_1</dt>
-<dd><p>Modified Rankin scale score at follow-up</p></dd>
-
-<dt>mrs_6</dt>
-<dd><p>Modified Rankin scale score at end of study</p></dd>
-
-<dt>hypertension</dt>
-<dd><p>Known hypertension</p></dd>
-
-<dt>diabetes</dt>
-<dd><p>Known diabetes</p></dd>
-
-<dt>civil</dt>
-<dd><p>Cohabitation status</p></dd>
-
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p><a href="https://doi.org/10.1161/STROKEAHA.117.020067" class="external-link">doi:10.1161/STROKEAHA.117.020067</a></p>
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docs/reference/win_prob.html

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-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the probability of winning (winP). In the referenced
-article Zou et al (2022) proposes a method for calculating probability of
-winning with a confidence interval an p-value testing."><title>Calculates the probability of winning — win_prob • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the probability of winning — win_prob"><meta property="og:description" content="Calculates the probability of winning (winP). In the referenced
-article Zou et al (2022) proposes a method for calculating probability of
-winning with a confidence interval an p-value testing."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-      <img src="../logo.png" class="logo" alt=""><h1>Calculates the probability of winning</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/win_prob.R" class="external-link"><code>R/win_prob.R</code></a></small>
-      <div class="d-none name"><code>win_prob.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Calculates the probability of winning (winP). In the referenced
-article Zou et al (2022) proposes a method for calculating probability of
-winning with a confidence interval an p-value testing.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">win_prob</span><span class="op">(</span></span>
-<span>  <span class="va">data</span>,</span>
-<span>  response <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  group <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  alpha <span class="op">=</span> <span class="fl">0.05</span>,</span>
-<span>  beta <span class="op">=</span> <span class="fl">0.2</span>,</span>
-<span>  group.ratio <span class="op">=</span> <span class="fl">1</span>,</span>
-<span>  sample.size <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  print.tables <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  dec <span class="op">=</span> <span class="fl">3</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p><a href="https://doi.org/10.1161/STROKEAHA.121.037744" class="external-link">doi:10.1161/STROKEAHA.121.037744</a></p>
-    </div>
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>data</dt>
-<dd><p>A data frame containing the response and group variable.</p></dd>
-
-
-<dt>response</dt>
-<dd><p>The name of the response variable.
-Takes first column if empty.</p></dd>
-
-
-<dt>group</dt>
-<dd><p>The name of the group variable.
-Takes second column if empty.</p></dd>
-
-
-<dt>alpha</dt>
-<dd><p>The alpha level for the hypothesis test. Default is 0.05.</p></dd>
-
-
-<dt>beta</dt>
-<dd><p>The beta level for the sample size calculation. Default is 0.2.</p></dd>
-
-
-<dt>group.ratio</dt>
-<dd><p>The ratio of group sizes. Default is 1.</p></dd>
-
-
-<dt>sample.size</dt>
-<dd><p>Flag to include sample size calculation. Default is FALSE.</p></dd>
-
-
-<dt>print.tables</dt>
-<dd><p>Flag to print cumulative tables. Default is FALSE.</p></dd>
-
-
-<dt>dec</dt>
-<dd><p>Numeric for decimals to print. Default is 3.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list containing the win_prob statistics.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">win_prob</span><span class="op">(</span>data<span class="op">=</span><span class="fu">stRoke</span><span class="fu">::</span><span class="va"><a href="talos.html">talos</a></span>,response<span class="op">=</span><span class="st">"mrs_6"</span>,group<span class="op">=</span><span class="st">"rtreat"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 	 Zou et al's winP (doi: 10.1161/STROKEAHA.121.037744) </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Probability of a random observation in Placebo group </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       will have a higher response score than a random</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       observation in Active group:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   	   winP: 0.400 (0.612, 0.372)      p=0.0125</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> --------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> The numbers needed to treat (NNT) are: -9</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-</code></pre></div>
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docs/reference/write_ical.html

@@ -1,199 +0,0 @@
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-Export as .ics file using calendar::ic_write()."><title>Write ical object — write_ical • stRoke</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Write ical object — write_ical"><meta property="og:description" content="This function creates an ical file based on a data frame with mixed events.
-Export as .ics file using calendar::ic_write()."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Write ical object</h1>
-      <small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/R/write_ical.R" class="external-link"><code>R/write_ical.R</code></a></small>
-      <div class="d-none name"><code>write_ical.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>This function creates an ical file based on a data frame with mixed events.
-Export as .ics file using <code><a href="https://rdrr.io/pkg/calendar/man/ic_write.html" class="external-link">calendar::ic_write()</a></code>.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">write_ical</span><span class="op">(</span></span>
-<span>  <span class="va">df</span>,</span>
-<span>  date <span class="op">=</span> <span class="st">"date"</span>,</span>
-<span>  date.end <span class="op">=</span> <span class="cn">NA</span>,</span>
-<span>  title <span class="op">=</span> <span class="st">"title"</span>,</span>
-<span>  time.start <span class="op">=</span> <span class="st">"start"</span>,</span>
-<span>  time.end <span class="op">=</span> <span class="st">"end"</span>,</span>
-<span>  place <span class="op">=</span> <span class="cn">NA</span>,</span>
-<span>  place.def <span class="op">=</span> <span class="cn">NA</span>,</span>
-<span>  time.def <span class="op">=</span> <span class="st">"10:00:00"</span>,</span>
-<span>  time.dur <span class="op">=</span> <span class="fl">60</span>,</span>
-<span>  descr <span class="op">=</span> <span class="cn">NA</span>,</span>
-<span>  link <span class="op">=</span> <span class="cn">NA</span>,</span>
-<span>  t.zone <span class="op">=</span> <span class="st">"CET"</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>df</dt>
-<dd><p>A data frame with the calendar data</p></dd>
-
-
-<dt>date</dt>
-<dd><p>The name of the event date column in the data frame</p></dd>
-
-
-<dt>date.end</dt>
-<dd><p>The name of the end date column in the data frame</p></dd>
-
-
-<dt>title</dt>
-<dd><p>The name of the title column in the data frame</p></dd>
-
-
-<dt>time.start</dt>
-<dd><p>The name of the start time column in the data frame</p></dd>
-
-
-<dt>time.end</dt>
-<dd><p>The name of the end time column in the data frame</p></dd>
-
-
-<dt>place</dt>
-<dd><p>The name of the place column in the data frame</p></dd>
-
-
-<dt>place.def</dt>
-<dd><p>Default location to use when place is NA</p></dd>
-
-
-<dt>time.def</dt>
-<dd><p>Default start time to use when time.start is NA</p></dd>
-
-
-<dt>time.dur</dt>
-<dd><p>Default duration of the event in minutes, if time.end is NA</p></dd>
-
-
-<dt>descr</dt>
-<dd><p>Name of description/notes column if any.</p></dd>
-
-
-<dt>link</dt>
-<dd><p>Name of link column, if any.</p></dd>
-
-
-<dt>t.zone</dt>
-<dd><p>A character string of time zone for events. The string must be
-a time zone that is recognized by the user's OS.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>ical object</p>
-    </div>
-    <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><a href="https://github.com/ATFutures/calendar/" class="external-link">calendar package</a>
-<a href="https://icalendar.org" class="external-link">icalendar standard webpage</a></p></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
-<span class="r-in"><span>  date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"2020-02-10"</span>, <span class="st">"2020-02-11"</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  date.end <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"2020-02-13"</span>,<span class="cn">NA</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Conference"</span>, <span class="st">"Lunch"</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"12:00:00"</span>, <span class="cn">NA</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  time.end <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"13:00:00"</span>, <span class="cn">NA</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  note <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Hi there"</span>,<span class="st">"Remember to come"</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  link <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"https://icalendar.org"</span>,<span class="st">"https://agdamsbo.github.io/stRoke/"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="fu">write_ical</span><span class="op">(</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span>,</span></span>
-<span class="r-in"><span>  date <span class="op">=</span> <span class="st">"date"</span>,</span></span>
-<span class="r-in"><span>  date.end <span class="op">=</span> <span class="st">"date.end"</span>,</span></span>
-<span class="r-in"><span>  title <span class="op">=</span> <span class="st">"title"</span>,</span></span>
-<span class="r-in"><span>  time.start <span class="op">=</span> <span class="st">"start"</span>,</span></span>
-<span class="r-in"><span>  time.end <span class="op">=</span> <span class="st">"time.end"</span>,</span></span>
-<span class="r-in"><span>  place.def <span class="op">=</span> <span class="st">"Conference Room"</span>,</span></span>
-<span class="r-in"><span>  descr <span class="op">=</span> <span class="st">"note"</span>,</span></span>
-<span class="r-in"><span>  link <span class="op">=</span> <span class="st">"link"</span></span></span>
-<span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 7</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   SUMMARY    DTSTART             DTEND               UID          LOCATION URL  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Conference 2020-02-10 <span style="color: #949494;">12:00:00</span> 2020-02-13 <span style="color: #949494;">13:00:00</span> ical-0544cc… Confere… http…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Lunch      2020-02-11 <span style="color: #949494;">10:00:00</span> 2020-02-11 <span style="color: #949494;">11:00:00</span> ical-62a024… Confere… http…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: DESCRIPTION &lt;chr&gt;</span></span>
-<span class="r-in"><span></span></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Andreas Gammelgaard Damsbo.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
-
-    </footer></div>
-
-  
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-  
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-  </body></html>
-

docs/sitemap.xml

@@ -1,117 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
-  <url>
-    <loc>/404.html</loc>
-  </url>
-  <url>
-    <loc>/LICENSE-text.html</loc>
-  </url>
-  <url>
-    <loc>/articles/Simple REDCap workflow.html</loc>
-  </url>
-  <url>
-    <loc>/articles/Toolbox.html</loc>
-  </url>
-  <url>
-    <loc>/articles/ds2dd.html</loc>
-  </url>
-  <url>
-    <loc>/articles/index.html</loc>
-  </url>
-  <url>
-    <loc>/articles/redcap.html</loc>
-  </url>
-  <url>
-    <loc>/authors.html</loc>
-  </url>
-  <url>
-    <loc>/index.html</loc>
-  </url>
-  <url>
-    <loc>/news/index.html</loc>
-  </url>
-  <url>
-    <loc>/reference/age_calc.html</loc>
-  </url>
-  <url>
-    <loc>/reference/ci_plot.html</loc>
-  </url>
-  <url>
-    <loc>/reference/color_plot.html</loc>
-  </url>
-  <url>
-    <loc>/reference/contrast_text.html</loc>
-  </url>
-  <url>
-    <loc>/reference/cpr_check.html</loc>
-  </url>
-  <url>
-    <loc>/reference/cpr_dob.html</loc>
-  </url>
-  <url>
-    <loc>/reference/cpr_female.html</loc>
-  </url>
-  <url>
-    <loc>/reference/cprs.html</loc>
-  </url>
-  <url>
-    <loc>/reference/ds2dd.html</loc>
-  </url>
-  <url>
-    <loc>/reference/files_filter.html</loc>
-  </url>
-  <url>
-    <loc>/reference/generic_stroke.html</loc>
-  </url>
-  <url>
-    <loc>/reference/gt_plot.html</loc>
-  </url>
-  <url>
-    <loc>/reference/index.html</loc>
-  </url>
-  <url>
-    <loc>/reference/index_plot.html</loc>
-  </url>
-  <url>
-    <loc>/reference/label_select.html</loc>
-  </url>
-  <url>
-    <loc>/reference/metadata_names.html</loc>
-  </url>
-  <url>
-    <loc>/reference/plot_olr.html</loc>
-  </url>
-  <url>
-    <loc>/reference/plot_ord_odds.html</loc>
-  </url>
-  <url>
-    <loc>/reference/print.win_Prob.html</loc>
-  </url>
-  <url>
-    <loc>/reference/quantile_cut.html</loc>
-  </url>
-  <url>
-    <loc>/reference/read_redcap_data.html</loc>
-  </url>
-  <url>
-    <loc>/reference/read_redcap_tables.html</loc>
-  </url>
-  <url>
-    <loc>/reference/score.html</loc>
-  </url>
-  <url>
-    <loc>/reference/source_lines.html</loc>
-  </url>
-  <url>
-    <loc>/reference/stRoke-package.html</loc>
-  </url>
-  <url>
-    <loc>/reference/talos.html</loc>
-  </url>
-  <url>
-    <loc>/reference/win_prob.html</loc>
-  </url>
-  <url>
-    <loc>/reference/write_ical.html</loc>
-  </url>
-</urlset>

inst/WORDLIST

@@ -1,4 +1,5 @@
 Andreas
+CMD
 Changelog
 Codecov
 DDMMYY
@@ -7,11 +8,13 @@ DataDictionary
 Gammelgaard
 Github
 Kraglund
+Labelling
 METACRAN
 NA's
 OLR
 ORCID
 OpenAI's
+PASE
 REDCap
 REDCapRITS
 RStudio
@@ -21,6 +24,7 @@ StackOverflow
 Sys
 TALOS
 Vectorised
+Washburn
 XXXX
 Zou
 agdamsbo

man/pase.Rd

@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pase.R
+\docType{data}
+\name{pase}
+\alias{pase}
+\title{Data frame with sample data of PASE score questionnaire}
+\format{
+A data frame with 200 rows and 21 variables:
+\describe{
+\item{sample_pase01}{item 01, factor}
+\item{sample_pase01b}{item 01b, factor}
+\item{sample_pase02}{item 02, factor}
+\item{sample_pase02a}{item 02a, factor}
+\item{sample_pase03}{item 03, factor}
+\item{sample_pase03b}{item 03b, factor}
+\item{sample_pase04}{item 04, factor}
+\item{sample_pase04b}{item 04b, factor}
+\item{sample_pase05}{item 05, factor}
+\item{sample_pase05b}{item 05b, factor}
+\item{sample_pase06}{item 06, factor}
+\item{sample_pase06b}{item 06b, factor}
+\item{sample_pase07}{item 07, factor}
+\item{sample_pase08}{item 08, factor}
+\item{sample_pase09a}{item 09a, factor}
+\item{sample_pase09b}{item 09b, factor}
+\item{sample_pase09c}{item 09c, factor}
+\item{sample_pase09d}{item 09d, factor}
+\item{sample_pase10}{item 10, factor}
+\item{sample_pase10a}{item 10a, numeric}
+\item{sample_pase10b}{item 10b, factor}
+}
+}
+\usage{
+data(pase)
+}
+\description{
+Contains non-identifiable organic trial data.
+Sample data labels are in Danish.
+}
+\keyword{datasets}

man/pase_calc.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pase_calc.R
+\name{pase_calc}
+\alias{pase_calc}
+\title{PASE score calculator}
+\usage{
+pase_calc(ds, adjust_work = FALSE)
+}
+\arguments{
+\item{ds}{data set}
+
+\item{adjust_work}{flag to set whether to include 10b type 1.
+Default is TRUE.}
+}
+\value{
+data.frame
+}
+\description{
+Calculates PASE score from raw questionnaire data.
+}
+\details{
+Labelling should be as defined by the questionnaire.
+02-06 should start with 0:3, 02a-06b should start with 1:4.
+\subsection{Regarding work scoring}{
+
+The score calculation manual available for the PASE questionnaire, all types
+of work should be included. According to the article by
+Washburn RA. et al (1999) sitting work is not included in the item 10 score.
+This differentiation is added with the option to set \code{adjust_work} to
+exclude item 10b category 1 work (set \code{TRUE}).
+}
+
+\subsection{Regarding output}{
+
+Output includes sub scores as well as sums, but also to columns assessing data
+quality and completeness. If any field has not been filled, \code{score_incompletes}
+will return \code{TRUE}. If all measures are missing \code{score_missings} is \code{TRUE}.
+If \code{adjust_work==TRUE}, 10b has to be filled, or \code{score_incompletes} will be
+set \code{TRUE}.
+}
+}
+\examples{
+summary(pase_calc(stRoke::pase)[,13])
+
+}

tests/testthat/test-pase_calc.R

@@ -0,0 +1,4 @@
+test_that("pase_calc works", {
+  expect_equal(median(pase_calc(stRoke::pase)[,13],na.rm=TRUE), 128.625)
+  expect_equal(median(pase_calc(stRoke::pase,TRUE)[,13],na.rm=TRUE), 116.2)
+})