see NEWS.md. redcap_read_tables() is out for now.

.Rbuildignore

@@ -14,3 +14,4 @@
 ^data-raw$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^drafts$

.gitignore

@@ -59,3 +59,5 @@ data/*.R
 .Rbuildignore
 
 inst/doc
+
+drafts/

DESCRIPTION

@@ -1,15 +1,19 @@
 Package: stRoke
-Title: Clinical Stroke Research Toolbox
+Title: Clinical Stroke Research
-Version: 23.1.6
+Version: 23.1.7
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))
+Author:
+    Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>,
+    Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>,
+    Becker (2020) <doi:10.18637/jss.v093.i02>
 Description: 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.
+    This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added.
     Versioning follows months and year. See NEWS.md for release notes.
-URL: https://agdamsbo.github.io/stRoke/, https://github.com/agdamsbo/stRoke, https://agdamsbo.github.io/neuRo-group/
+URL: https://agdamsbo.github.io/stRoke/, https://github.com/agdamsbo/stRoke
 BugReports: https://github.com/agdamsbo/stRoke/issues
 License: GPL-3
 Encoding: UTF-8
@@ -18,26 +22,20 @@ RoxygenNote: 7.2.3
 LazyData: true
 Suggests:
     knitr,
-    REDCapRITS (>= 0.2.2.1),
-    remotes,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0)
 Language: en-US
 Config/testthat/edition: 3
 Imports: 
-    cli,
     dplyr,
     ggplot2,
     gtsummary,
     MASS,
     rankinPlot,
-    REDCapR,
     stats,
     tidyr,
     utils
 Depends: 
     R (>= 2.10)
-Remotes: 
-    agdamsbo/REDCapRITS
 VignetteBuilder: knitr

NAMESPACE

@@ -10,7 +10,6 @@ export(generic_stroke)
 export(index_plot)
 export(label_select)
 export(quantile_cut)
-export(read_redcap_tables)
 export(source_lines)
 export(win_prob)
 import(ggplot2)

NEWS.md

@@ -1,41 +1,49 @@
-# stRoke 23.1.6
+# stRoke 23.1.7
 
-## New ttempt at CRAN submission
+### Functions:
 
-## Functions:
+* redcap_read_tables() has been removed from the package for now. Looking to add it back later as a minimal data acquisition tool.
+
+# stRoke 23.1.6 - failed due to dependencies
+
+### New attempt at CRAN submission
+
+### Functions:
 
 * win_prop() added to implement the suggested methods in [DOI: 10.1161/STROKEAHA.121.037744](https://doi.org/10.1161/STROKEAHA.121.037744), as an implementation of "Tournament Methods" also found in `library(genodds)`. The function is based on the spreadsheet provided by the authors. A print.win_Prop is also added for printing.
 
-## Notes:
+### Notes:
 
 * 23.1.5 failed on CRAN due to gt_plot(). This function has been dropped. Find it as as_ggplot() elsewhere.
+* agdamsbo/REDCapRITS added as "Additional_repositories".
+* Included references listed as authors.
 
 # stRoke 23.1.5
 
-## RELEASE ON CRAN - failed
+### RELEASE ON CRAN - failed
 
 # stRoke 0.23.1.4
 
-## Functions:
+### Functions:
 
 * plot_olr() has been deprecated and removed. 
 * ci_plot() functionality extended to include logistic model plotting.
 * age_calc() use vapply() instead of sapply()
 * gt_plot() function added to plot gt elements as ggplots. From [bstfun](https://github.com/MSKCC-Epi-Bio/bstfun). Not all done and satisfied with the layout with patchwork.
 
-## Documentation
+### Documentation
 
 * Trying to complete all flags from goodpractice and inteRgrate
 
 # stRoke 0.23.1.3
 
-## Functions:
+### Functions:
 
 * files_filter() added. Simple function to get file names in path with specified filter.
 * updated cpr_dob to give warnings if format is not recognised and return NAs.
 * ci_plot() updated to actually handle binary factors. Uses glm(), not lm().
 
-## Documentation:
+### Documentation:
 
 * test, test and tests to satisfy codecov and, of course, ensure higher quality
 * changes to comply with goodpractices::gp()
@@ -44,27 +52,27 @@
 
 # stRoke 0.23.1.2
 
-## Functions:
+### Functions:
 
 * cpr_dob() now includes `format=`.
 * Other minor updates.
 
-## Documentation:
+### Documentation:
 
 * Two new vignettes
 * Taking last steps in documenting before releasing on CRAN
 
-## Other:
+### Other:
 
 * New hex logo
 
 # stRoke 0.23.1.1
 
-## Functions:
+### Functions:
 
 * age_calc() now also outputs a numeric vector for units="days", and not a character vector as difftime() would.
 
-## Documentation:
+### Documentation:
 
 * Added a `NEWS.md` file to track changes to the package.
 * Added codecov

R/cprs.R

@@ -7,7 +7,7 @@
 #' \describe{
 #'   \item{cpr}{Mixed format cpr-numbers, characters}
 #' }
-#' @source \url{https://da.wikipedia.org/wiki/231045-0637}
+#' @seealso \url{https://da.wikipedia.org/wiki/231045-0637}
 #' @usage data(cprs)
 "cprs"
 

R/read_redcap_tables.R

@@ -1,71 +0,0 @@
-#' Download REDCap data
-#' 
-#' Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split 
-#' including some clean-up. Works with longitudinal projects with repeating 
-#' instruments.
-#' @param uri REDCap database uri
-#' @param token API token
-#' @param records records to download
-#' @param fields fields to download
-#' @param events events to download
-#' @param forms forms to download
-#' @param generics vector of auto-generated generic variable names to 
-#' ignore when discarding empty rows
-#'
-#' @return list of instruments
-#' @export 
-#'
-#' @examples
-#' # Examples will be provided later
-read_redcap_tables <- function(uri,
-                               token,
-                               records = NULL,
-                               fields = NULL,
-                               events = NULL,
-                               forms = NULL,
-                               generics = c(
-                                 "record_id",
-                                 "redcap_event_name",
-                                 "redcap_repeat_instrument",
-                                 "redcap_repeat_instance"
-                               )) {
-  # Notes to self: Based on the metadata, this functionality could be 
-  # introduced without using the REDCapRITS package.. To be tried..
-  
-  d <- REDCapR::redcap_read (
-    redcap_uri = uri,
-    token = token,
-    fields = fields,
-    events = events,
-    forms = forms,
-    records = records
-  )
-  
-  m <-
-    REDCapR::redcap_metadata_read (redcap_uri = uri, token = token)
-  
-  if (requireNamespace("REDCapRITS", quietly = TRUE)) {
-    l <- REDCapRITS::REDCap_split(d$data,
-                                  m$data[m$data$field_name %in% names(d$data),],
-                                  forms = "all")
-  } else {
-    cli::cli_abort(
-      c(
-        "x" = "The package REDCapRITS is not installed.",
-        "i" = "Please install REDCapRITS by running
-        \"remotes::install_github('agdamsbo/REDCapRITS')\"."
-      )
-    )
-  }
-  
-  lapply(l, function(i) {
-    if (ncol(i) > 2) {
-      s <- data.frame(i[, !colnames(i) %in% generics])
-      i[!apply(is.na(s), MARGIN = 1, FUN = all),]
-    } else {
-      i
-    }
-  })
-  
-}
-

R/win_prob.R

@@ -13,8 +13,7 @@
 #' @param sample.size Flag to include sample size calculation. Default is FALSE.
 #' @param print.tables Flag to print cumulative tables. Default is FALSE.
 #' @param dec Numeric for decimals to print. Default is 3.
-#' @return A list containing the win_prob statistic, the confidence interval,
+#' @return A list containing the win_prob statistics.
-#' and the p-value.
 #' @export
 #' @importFrom stats pnorm qnorm xtabs
 #' @source \doi{10.1161/STROKEAHA.121.037744}

man/cprs.Rd

@@ -10,9 +10,6 @@ A data frame with 200 rows and 1 variable:
 \item{cpr}{Mixed format cpr-numbers, characters}
 }
 }
-\source{
-\url{https://da.wikipedia.org/wiki/231045-0637}
-}
 \usage{
 data(cprs)
 }
@@ -20,4 +17,7 @@ data(cprs)
 This is just a repeated sample of 8 synthesized cpr-numbers
 for testing purposes.
 }
+\seealso{
+\url{https://da.wikipedia.org/wiki/231045-0637}
+}
 \keyword{datasets}

man/read_redcap_tables.Rd

@@ -1,44 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_redcap_tables.R
-\name{read_redcap_tables}
-\alias{read_redcap_tables}
-\title{Download REDCap data}
-\usage{
-read_redcap_tables(
-  uri,
-  token,
-  records = NULL,
-  fields = NULL,
-  events = NULL,
-  forms = NULL,
-  generics = c("record_id", "redcap_event_name", "redcap_repeat_instrument",
-    "redcap_repeat_instance")
-)
-}
-\arguments{
-\item{uri}{REDCap database uri}
-
-\item{token}{API token}
-
-\item{records}{records to download}
-
-\item{fields}{fields to download}
-
-\item{events}{events to download}
-
-\item{forms}{forms to download}
-
-\item{generics}{vector of auto-generated generic variable names to
-ignore when discarding empty rows}
-}
-\value{
-list of instruments
-}
-\description{
-Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
-including some clean-up. Works with longitudinal projects with repeating
-instruments.
-}
-\examples{
-# Examples will be provided later
-}

man/stRoke-package.Rd

@@ -4,16 +4,15 @@
 \name{stRoke-package}
 \alias{stRoke}
 \alias{stRoke-package}
-\title{stRoke: Clinical Stroke Research Toolbox}
+\title{stRoke: Clinical Stroke Research}
 \description{
-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. Versioning follows months and year. See NEWS.md for release notes.
+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. Versioning follows months and year. See NEWS.md for release notes.
 }
 \seealso{
 Useful links:
 \itemize{
   \item \url{https://agdamsbo.github.io/stRoke/}
   \item \url{https://github.com/agdamsbo/stRoke}
-  \item \url{https://agdamsbo.github.io/neuRo-group/}
   \item Report bugs at \url{https://github.com/agdamsbo/stRoke/issues}
 }
 

man/win_prob.Rd

@@ -41,8 +41,7 @@ Takes second column if empty.}
 \item{dec}{Numeric for decimals to print. Default is 3.}
 }
 \value{
-A list containing the win_prob statistic, the confidence interval,
+A list containing the win_prob statistics.
-and the p-value.
 }
 \description{
 Calculates the probability of winning (winP)

tests/testthat/test-read_redcap_tables.R

@@ -1,7 +0,0 @@
-# Unit Test
-
-# Test that the function throws an error when uri and token are not provided
-test_that("read_redcap_tables throws error when uri and token are not provided",
-          {
-            testthat::expect_error(read_redcap_tables(uri, token))
-          })

vignettes/redcap.Rmd

@@ -1,55 +0,0 @@
----
-title: "Simple REDCap workflow"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Simple REDCap workflow}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-```
-
-```{r setup}
-library(stRoke)
-```
-
-# Initial note
-
-Please refer to the book ["neuRo-group"](https://agdamsbo.github.io/neuRo-group/) for a more thorough guide on using R and REDCap together in data analysis, but also for notes and advices on how to build a REDCap database. Note, that this book is a work in progress with no goal of "completion".
-
-# Working with data from REDCap
-
-[REDCap](https://www.project-redcap.org) is an excellent tool for clinical data acquisition and storage. It is widely used world wide and is the standard tool for medical research data in Denmark.
-
-In the case of analysing data directly whole storing data in REDCap, the API functionality is very convenient and secure, as you are not storing (possibly) sensitive data permanently on your computer.
-
-When using the "events" or "repeated instruments" functionality of REDCap, the data storage format is a little confusing to work with, when being accustomed to tidy data.
-
-The [`library(REDCapR)`](https://ouhscbbmc.github.io/REDCapR/) provides a simple way of working with data, however, the package just exports data in standard format.
-
-## Examples
-
-```{r redcapr-focused, eval=FALSE}
-library(REDCapR)
-# Returns the variables "record_id" and "age".
-ds_some_vars <- redcap_read(
-  redcap_uri   = "https://redcap.au.dk/api/",
-  # This is the address for projects at the AU-server
-  token        = "YOUR_API_KEY_GOES_HERE",
-  fields       = c("record_id", "age")
-)$data
-
-# Return only records with IDs of 1 and 4
-ds_some_rows <- redcap_read(redcap_uri   = "https://redcap.au.dk/api/",
-                            # This is the address for projects at the AU-server
-                            token        = "YOUR_API_KEY_GOES_HERE",
-                            records      = c(1, 4))$data
-```
-
-
-_more will be added_

vignettes/toolbox.Rmd

@@ -124,12 +124,6 @@ Used for plotting scores from a multi dimensional patient test.
 index_plot(stRoke::score[score$event == "A", ])
 ```
 
-### read_redcap_tables()
-
-Reads REDCap data accounting for events and repeated instruments. Based on `library(REDCapR)` and `library(agdamsbo/REDCapRITS)`.
-
-Please see [the vignette on REDCap](https://agdamsbo.github.io/stRoke/articles/redcap.html).
-
 ### win_prob()
 
 The `win_prob()` is an implementation of the Tournament Method for calculating the probability of winning as suggested by [Zou et al 2022](https://doi.org/10.1161/STROKEAHA.121.037744). The authors has included a spreadsheet as supplementary materials. This function aims to mimic that functionality. The function also includes a `print()` extension for nice printing.