new function including sample data

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: stRoke
 Title: Tools for work in clinical stroke research
-Version: 0.22.10.1
+Version: 0.22.11.1
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))
@@ -18,8 +18,12 @@ Suggests:
 Language: en-US
 Config/testthat/edition: 3
 Imports: 
+    dplyr,
     ggplot2,
     gtsummary,
     MASS,
     rankinPlot,
-    stats
+    stats,
+    tidyr
+Depends: 
+    R (>= 2.10)

NAMESPACE

@@ -6,12 +6,17 @@ export(cpr_check)
 export(cpr_dob)
 export(cpr_female)
 export(generic_stroke)
+export(index_plot)
 export(plot_olr)
 export(quantile_cut)
 export(source_lines)
 import(ggplot2)
 import(stats)
+import(tidyr)
 importFrom(MASS,polr)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,select)
 importFrom(gtsummary,add_overall)
 importFrom(gtsummary,tbl_summary)
 importFrom(rankinPlot,grottaBar)

R/index_plot.R

@@ -0,0 +1,74 @@
+utils::globalVariables(c("name","value","facet"))
+#' Plot multidimensional cognitive test scores
+#' 
+#' Plot index scores from five dimensional cognitive testing. Includes option to facet.
+#'
+#' @param ds complete data frame
+#' @param id colname of id column. Base for colouring
+#' @param sub_plot main outcome scores variable to plot
+#' @param scores variables to subset for plotting. Has to follow standard naming (is to be changed)
+#' @param dom_names domain names for axis naming
+#' @param facet.by variable to base facet_grid on
+#'
+#' @return ggplot element
+#' 
+#' @import ggplot2 tidyr
+#' @importFrom dplyr mutate
+#' @importFrom dplyr select
+#' @importFrom dplyr filter
+#' 
+#' @export
+#'
+#' @examples
+#' data(score)
+#' index_plot(score |> dplyr::filter(event=="A"))
+index_plot <- function(ds,id="id",sub_plot="_is",scores=c("_is","_lo","_up","_per"),dom_names=c("immediate","visuospatial","verbal","attention","delayed","total"),facet.by=NULL){
+
+  df_plot<-ds|>
+    dplyr::select(c(id,
+             facet.by,
+             ends_with(scores)))|>
+    tidyr::pivot_longer(cols=-c(id,facet.by))|>
+    subset(grepl(sub_plot,name))|>
+    dplyr::mutate(value=as.numeric(value),
+           name=factor(name,labels = dom_names))
+  
+  if (!is.null(facet.by)){
+    colnames(df_plot)<-c("id","facet","name","value")
+  } else {
+    colnames(df_plot)<-c("id","name","value")
+  }
+  
+  if (sub_plot=="_is"){
+    index_plot<-df_plot|>
+      ggplot2::ggplot(mapping = ggplot2::aes(x=name, y=value, color=factor(id), group=factor(id))) + 
+      ggplot2::geom_point() +
+      ggplot2::geom_path() +
+      ggplot2::expand_limits(y=c(40,160)) +
+      ggplot2::scale_y_continuous(breaks=seq(40,160,by=10)) +
+      ggplot2::ylab("Index Score") +
+      ggplot2::xlab("Domain")+
+      ggplot2::labs(colour = "ID")
+  }
+  
+  if (sub_plot=="_per"){
+    index_plot<-df_plot|>
+      ggplot2::ggplot(mapping = ggplot2::aes(x=name, y=value, fill=factor(id)))+
+      ggplot2::geom_col(position = "dodge") +
+      ggplot2::expand_limits(y=c(0,100)) +
+      ggplot2::scale_y_continuous(breaks=seq(0,100,by=10)) +
+      ggplot2::xlab("Cognitive domains") +
+      ggplot2::ylab("Percentile") + 
+      ggplot2::labs(fill = "ID")
+  }
+  
+  if (!is.null(facet.by)){
+    index_plot + facet_grid(cols=vars(facet)) +
+      ggplot2::theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) 
+    
+  } else {
+    index_plot
+  }
+  
+}
+

R/score.R

@@ -0,0 +1,36 @@
+#' Data frame with sample data of cognitive testing score
+#'
+#' Contains non-identifiable organic trial data from a five-dimensional cognitive test.
+#'
+#' @format A data frame with 20 rows and 26 variables:
+#' \describe{
+#'   \item{id}{id}
+#'   \item{event}{event}
+#'   \item{a_is}{domain a index score}
+#'   \item{b_is}{domain b index score}
+#'   \item{c_is}{domain c index score}
+#'   \item{d_is}{domain d index score}
+#'   \item{e_is}{domain e index score}
+#'   \item{i_is}{total index score}
+#'   \item{a_lo}{domain a lower ci}
+#'   \item{b_lo}{domain b lower ci}
+#'   \item{c_lo}{domain c lower ci}
+#'   \item{d_lo}{domain d lower ci}
+#'   \item{e_lo}{domain e lower ci}
+#'   \item{i_lo}{total lower ci}
+#'   \item{a_up}{domain a upper ci}
+#'   \item{b_up}{domain b upper ci}
+#'   \item{c_up}{domain c upper ci}
+#'   \item{d_up}{domain d upper ci}
+#'   \item{e_up}{domain e upper ci}
+#'   \item{i_up}{total upper ci}
+#'   \item{a_per}{domain a percentile}
+#'   \item{b_per}{domain b percentile}
+#'   \item{c_per}{domain c percentile}
+#'   \item{d_per}{domain d percentile}
+#'   \item{e_per}{domain e percentile}
+#'   \item{i_per}{total percentile}
+#' }
+#' @usage data(score)
+"score"
+

R/talos.R

@@ -2,7 +2,7 @@
 #'
 #' Contains of non-identifiable data from the [TALOS trial](https://doi.org/10.1161/STROKEAHA.117.020067/)
 #'
-#' @format A data frame with 200 rows and 1 variable:
+#' @format A data frame with 200 rows and 6 variables:
 #' \describe{
 #'   \item{rtreat}{Randomisation}
 #'   \item{mrs_1}{Modified Rankin scale score at follow-up}

inst/WORDLIST

@@ -7,22 +7,33 @@ ORCID
 Randomisation
 TALOS
 Vectorised
+af
 agdamsbo
+christophergandrud
+ci
+colname
+colouring
 cpr
 cprs
 daDoctoR
 ddmmyy
 ddmmyyxxxx
 df
+dk
+eb
+eg
 forrestplot
 gg
 ggplot
+github
 grotta
 grottaBar
+helpfull
 https
 mRS
 olr
 polr
+sst
 www
 xxxx
 yyyy

man/index_plot.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/index_plot.R
+\name{index_plot}
+\alias{index_plot}
+\title{Plot multidimensional cognitive test scores}
+\usage{
+index_plot(
+  ds,
+  id = "id",
+  sub_plot = "_is",
+  scores = c("_is", "_lo", "_up", "_per"),
+  dom_names = c("immediate", "visuospatial", "verbal", "attention", "delayed", "total"),
+  facet.by = NULL
+)
+}
+\arguments{
+\item{ds}{complete data frame}
+
+\item{id}{colname of id column. Base for colouring}
+
+\item{sub_plot}{main outcome scores variable to plot}
+
+\item{scores}{variables to subset for plotting. Has to follow standard naming (is to be changed)}
+
+\item{dom_names}{domain names for axis naming}
+
+\item{facet.by}{variable to base facet_grid on}
+}
+\value{
+ggplot element
+}
+\description{
+Plot index scores from five dimensional cognitive testing. Includes option to facet.
+}
+\examples{
+data(score)
+index_plot(score |> dplyr::filter(event=="A"))
+}

man/score.Rd

@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/score.R
+\docType{data}
+\name{score}
+\alias{score}
+\title{Data frame with sample data of cognitive testing score}
+\format{
+A data frame with 20 rows and 26 variables:
+\describe{
+\item{id}{id}
+\item{event}{event}
+\item{a_is}{domain a index score}
+\item{b_is}{domain b index score}
+\item{c_is}{domain c index score}
+\item{d_is}{domain d index score}
+\item{e_is}{domain e index score}
+\item{i_is}{total index score}
+\item{a_lo}{domain a lower ci}
+\item{b_lo}{domain b lower ci}
+\item{c_lo}{domain c lower ci}
+\item{d_lo}{domain d lower ci}
+\item{e_lo}{domain e lower ci}
+\item{i_lo}{total lower ci}
+\item{a_up}{domain a upper ci}
+\item{b_up}{domain b upper ci}
+\item{c_up}{domain c upper ci}
+\item{d_up}{domain d upper ci}
+\item{e_up}{domain e upper ci}
+\item{i_up}{total upper ci}
+\item{a_per}{domain a percentile}
+\item{b_per}{domain b percentile}
+\item{c_per}{domain c percentile}
+\item{d_per}{domain d percentile}
+\item{e_per}{domain e percentile}
+\item{i_per}{total percentile}
+}
+}
+\usage{
+data(score)
+}
+\description{
+Contains non-identifiable organic trial data from a five-dimensional cognitive test.
+}
+\keyword{datasets}

man/talos.Rd

@@ -5,7 +5,7 @@
 \alias{talos}
 \title{Data frame with sample of TALOS data}
 \format{
-A data frame with 200 rows and 1 variable:
+A data frame with 200 rows and 6 variables:
 \describe{
 \item{rtreat}{Randomisation}
 \item{mrs_1}{Modified Rankin scale score at follow-up}