major update with new functions and renv is out! see NEWS section

.Rprofile

@@ -6,7 +6,7 @@ options(
 )
 
 
-source("renv/activate.R")
+# source("renv/activate.R")
 
 if (interactive()) {
   suppressMessages(require(usethis))

.github/workflows/R-CMD-check.yaml

@@ -39,7 +39,7 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-renv@v2
+      # - uses: r-lib/actions/setup-renv@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/pkgdown.yaml

@@ -30,7 +30,7 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-renv@v2
+      # - uses: r-lib/actions/setup-renv@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/test-coverage.yaml

@@ -21,7 +21,7 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-renv@v2
+      # - uses: r-lib/actions/setup-renv@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 24.5.1
+Version: 24.6.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 

NEWS.md

@@ -1,4 +1,4 @@
-# REDCapCAST 24.5.1
+# REDCapCAST 24.6.1
 
 ### Functions
 

R/doc2dd.R

@@ -108,6 +108,9 @@ doc2dd <- function(data,
       )
   }
 
+
+
+
   ## Defining the calculations
   if (is_missing(col.calculation)) {
     out <- out |>
@@ -115,12 +118,13 @@ doc2dd <- function(data,
         calculations = missing.default
       )
   } else {
+    # With inspiration from textclean package, curly apostrophe is replaced
     out <- out |>
       dplyr::mutate(
         calculations = dplyr::pick(col.calculation) |>
           unlist() |>
           tolower() |>
-          (\(.x) gsub("’", "'", .x))()
+          replace_curly_quote()
       )
   }
 
@@ -288,3 +292,22 @@ is_missing <- function(data,nas=c("", "NA")) {
     is.na(data) | data %in% nas
   }
 }
+
+
+#' Replace curly apostrophes and quotes from word
+#'
+#' @description
+#' Copied from textclean, which has not been updated since 2018 and is not
+#' on CRAN. Github:https://github.com/trinker/textclean
+#'
+#' @param x character vector
+#'
+#' @return character vector
+replace_curly_quote <- function(x){
+  replaces <- c('\x91', '\x92', '\x93', '\x94')
+  Encoding(replaces) <- "latin1"
+  for (i in 1:4) {
+    x <- gsub(replaces[i], c("'", "'", "\"", "\"")[i], x, fixed = TRUE)
+  }
+  x
+}

R/ds2dd_detailed.R

@@ -343,10 +343,10 @@ ds2dd_detailed <- function(data,
       lapply(function(x) {
         if (is.factor(x)) {
           ## Re-factors to avoid confusion with missing levels
-          ## Assumes alle relevant levels are represented in the data
+          ## Assumes all relevant levels are represented in the data
           re_fac <- factor(x)
           paste(
-            paste(unique(as.numeric(re_fac)),
+            paste(seq_along(levels(re_fac)),
               levels(re_fac),
               sep = ", "
             ),

app/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 11351429
-bundleId:
+bundleId: 8567755
 url: https://agdamsbo.shinyapps.io/redcapcast/
 version: 1

app/ui.R

@@ -1,6 +1,6 @@
 ui <- shiny::shinyUI(
   shiny::fluidPage(
-    theme = shinythemes::shinytheme("united"),
+    theme = shinythemes::shinytheme("flatly"),
 
     ## -----------------------------------------------------------------------------
     ## Application title
@@ -11,15 +11,20 @@ ui <- shiny::shinyUI(
     #                   windowTitle = "REDCap database creator"
     # ),
 
-    shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
+    shiny::titlePanel(
-                                  "Easy REDCap database creation"),
+      title = shiny::div(
+        shiny::a(shiny::img(src = "logo.png"), href = "https://agdamsbo.github.io/REDCapCAST"),
+        "Easy REDCap database creation"
+      ),
       windowTitle = "REDCap database creator"
     ),
-    shiny::h4("This tool includes to convenient functions:",
+    shiny::h4(
+      "This tool includes to convenient functions:",
       shiny::br(),
       "1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
       shiny::br(),
-              "2) creating said database on a given REDCap server and uploading the dataset via API access."),
+      "2) creating said database on a given REDCap server and uploading the dataset via API access."
+    ),
 
 
     ## -----------------------------------------------------------------------------
@@ -60,7 +65,7 @@ ui <- shiny::shinyUI(
         label = "API key",
         value = ""
       ),
-      shiny::h6("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href="https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
+      shiny::h6("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href = "https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
       shiny::actionButton(
         inputId = "upload.meta",
         label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
@@ -112,13 +117,13 @@ ui <- shiny::shinyUI(
     shiny::tags$footer(shiny::strong("Disclaimer: "),
       "This tool is aimed at demonstrating use of REDCapCAST. No responsibility for data loss or any other problems will be taken. Please contact me for support.",
       shiny::br(),
-                       shiny::a("License: GPL-3+",href="https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
+      shiny::a("License: GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
       "|",
-                       shiny::a("agdamsbo/REDCapCAST",href="https://agdamsbo.github.io/REDCapCAST"),
+      shiny::a("agdamsbo/REDCapCAST", href = "https://agdamsbo.github.io/REDCapCAST"),
       "|",
-                       shiny::a("Source",href="https://github.com/agdamsbo/REDCapCAST"),
+      shiny::a("Source", href = "https://github.com/agdamsbo/REDCapCAST"),
       "|",
-                       shiny::a("Contact",href="https://andreas.gdamsbo.dk"),
+      shiny::a("Contact", href = "https://andreas.gdamsbo.dk"),
       align = "center",
       style = "
                  position:fixed;
@@ -129,6 +134,7 @@ ui <- shiny::shinyUI(
                  padding: 0px;
                  background-color: White;
                  z-index: 100;
-                ")
+                "
+    )
   )
 )

inst/WORDLIST

@@ -4,6 +4,7 @@ Codecov
 DOI
 DataDictionary
 GStat
+Github
 GithubActions
 JSON
 Lifecycle
@@ -14,7 +15,6 @@ README
 REDCap
 REDCapR
 REDCapRITS
-THe
 UI
 WD
 al
@@ -34,8 +34,10 @@ dplyr
 ds
 dta
 et
+github
 gues
 hms
+https
 immprovements
 io
 jbi
@@ -55,6 +57,7 @@ perl
 pos
 pre
 readr
+realising
 sel
 sep
 seperator
@@ -64,9 +67,11 @@ stRoke
 stata
 strsplit
 subheader
+textclean
 thorugh
 tibble
 tidyverse
+trinker
 ui
 uri
 wil

man/replace_curly_quote.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/doc2dd.R
+\name{replace_curly_quote}
+\alias{replace_curly_quote}
+\title{Replace curly apostrophes and quotes from word}
+\usage{
+replace_curly_quote(x)
+}
+\arguments{
+\item{x}{character vector}
+}
+\value{
+character vector
+}
+\description{
+Copied from textclean, which has not been updated since 2018 and is not
+on CRAN. Github:https://github.com/trinker/textclean
+}

renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.3",
+    "Version": "4.4.0",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -138,14 +138,14 @@
     },
     "cachem": {
       "Package": "cachem",
-      "Version": "1.0.8",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "fastmap",
         "rlang"
       ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -199,16 +199,6 @@
       "Repository": "CRAN",
       "Hash": "5d8225445acb167abf7797de48b2ee3c"
     },
-    "cpp11": {
-      "Package": "cpp11",
-      "Version": "0.4.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
-    },
     "crayon": {
       "Package": "crayon",
       "Version": "1.5.2",
@@ -279,10 +269,10 @@
     },
     "fastmap": {
       "Package": "fastmap",
-      "Version": "1.1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
     },
     "filelock": {
       "Package": "filelock",
@@ -533,13 +523,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.1.2",
+      "Version": "2.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "ea2475b073243d9d338aa8f086ce973e"
+      "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
     },
     "openxlsx2": {
       "Package": "openxlsx2",
@@ -585,30 +575,6 @@
       ],
       "Hash": "01f28d4278f15c76cddbea05899c5d6f"
     },
-    "prettyunits": {
-      "Package": "prettyunits",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
-    },
-    "progress": {
-      "Package": "progress",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "crayon",
-        "hms",
-        "prettyunits"
-      ],
-      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
-    },
     "promises": {
       "Package": "promises",
       "Version": "1.3.0",
@@ -785,7 +751,7 @@
     },
     "stringi": {
       "Package": "stringi",
-      "Version": "1.8.3",
+      "Version": "1.8.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -794,7 +760,7 @@
         "tools",
         "utils"
       ],
-      "Hash": "058aebddea264f4c99401515182e656a"
+      "Hash": "39e1144fd75428983dc3f63aa53dfa91"
     },
     "stringr": {
       "Package": "stringr",

tests/spelling.Rout.save

@@ -0,0 +1,25 @@
+
+R version 3.4.1 (2017-06-30) -- "Single Candle"
+Copyright (C) 2017 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin15.6.0 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> if(requireNamespace('spelling', quietly = TRUE))
++   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
++                              skip_on_cran = TRUE)
+All Done!
+>
+> proc.time()
+   user  system elapsed
+  0.372   0.039   0.408

vignettes/Database-creation.Rmd

@@ -18,33 +18,59 @@ knitr::opts_chunk$set(
 library(REDCapCAST)
 ```
 
-# Easy data set to data base workflow
+# Two different ways to create a data base
 
-THe first iteration of a dataset to data dictionary function is the `ds2dd()`, which creates a very basic data dictionary with all variables stored as text. This is sufficient for just storing old datasets/spreadsheets securely in REDCap.
+`REDCapCAST` provides two approaches to creating a data dictionary aimed at helping out in two different cases:
 
-```{r eval=FALSE}
+1.   Easily create a REDCap data base from an existing data set.
-mtcars |>
+
+2.   Create a table in Word describing a variables in a data base and use this to create a data base.
+
+In the following I will try to come with a few suggestions on how to use these approaches.
+
+## Easy data set to data base workflow
+
+The first iteration of a dataset to data dictionary function is the `ds2dd()`, which creates a very basic data dictionary with all variables stored as text. This is sufficient for just storing old datasets/spreadsheets securely in REDCap.
+
+```{r eval=TRUE}
+d1 <- mtcars |>
   dplyr::mutate(record_id = seq_len(dplyr::n())) |>
-  ds2dd() |>
+  ds2dd() 
-  str()
+
+d1 |>
+  gt::gt()
 ```
 
 The more advanced `ds2dd_detailed()` is a natural development. It will try to apply the most common data classes for data validation and will assume that the first column is the id number. It outputs a list with the dataset with modified variable names to comply with REDCap naming conventions and a data dictionary. 
 
 The dataset should be correctly formatted for the data dictionary to preserve as much information as possible.
 
-```{r eval=FALSE}
+```{r eval=TRUE}
-dd_ls <- mtcars |>
+d2 <- REDCapCAST::redcapcast_data |> 
-  dplyr::mutate(record_id = seq_len(dplyr::n())) |>
+  dplyr::mutate(record_id = seq_len(dplyr::n()),
+                region=factor(region)) |>
   dplyr::select(record_id, dplyr::everything()) |>
-  ds2dd_detailed()
+  (\(.x){
-dd_ls |> 
+    .x[!grepl("_complete$",names(.x))]
-  str()
+  })() |> 
+  (\(.x){
+    .x[!grepl("^redcap",names(.x))]
+  })() |>  
+  ds2dd_detailed() |> 
+  purrr::pluck("meta") 
+
+d2 |> 
+  gt::gt()
 ```
 
-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.
+Additional specifications to the DataDictionary can be made manually, or it can be uploaded and modified manually in the graphical user interface on the REDCap server.
 
-## Step 3 - Meta data upload
+## Data base from table
+
+
+
+
+## Meta data and data upload
 
 Now the DataDictionary can be exported as a spreadsheet and uploaded or it can be uploaded using the `REDCapR` package (only projects with "Development" status).
 

vignettes/Shiny-app.Rmd

@@ -14,10 +14,6 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r setup}
-library(REDCapCAST)
-```
-
 To make the easiest possible transition from spreadsheet/dataset to REDCap, I have created a small Shiny app, which adds a graphical interface to the casting of a data dictionary and data upload. Install the package and run the app as follows:
 
 ```{r eval=FALSE}