usethis::use_gpl_license(version = 2)

Author: sbalci

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPathDescriptives
 Title: Descriptives Functions for Clinicopathological Research
-Version: 0.0.2.26
-Date: 2024-01-19
+Version: 0.0.2.28
+Date: 2024-11-02
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -21,7 +21,7 @@ URL: https://github.com/sbalci/ClinicoPathJamoviModule/,
     https://sbalci.github.io/ClinicoPathJamoviModule/
 BugReports: 
     https://github.com/sbalci/ClinicoPathJamoviModule/issues/
-License: GPL-3
+License: GPL (>= 2)
 Depends:
     R (>= 4.1.0)
 Imports: 
@@ -50,10 +50,10 @@ Imports:
     shiny,
     gtsummary,
     gtExtras,
-    UpSetR
+    labelled
 Remotes:
     nbarrowman/vtree@ffa53d4ea5050fa9b26918f4bb30595e91a0f489
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

LICENSE.md

@@ -434,9 +434,17 @@
         `type`="software", 
         `author`="Linlin Yan", 
         `year`=2020, 
-        `title`=" Venn Diagram by ggplot2, with really easy-to-use API", 
+        `title`="Venn Diagram by ggplot2, with really easy-to-use API", 
         `publisher`="[R package]. Retrieved from https://github.com/yanlinlin82/ggvenn", 
         `url`="https://github.com/yanlinlin82/ggvenn"), 
+    `upset`=list(
+        `type`="software", 
+        `author`="Jake R Conway, Alexander Lex, Nils Gehlenborg", 
+        `year`=2017, 
+        `title`="UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties", 
+        `doi`="10.1093/bioinformatics/btx364", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=UpSetR", 
+        `url`="https://CRAN.R-project.org/package=UpSetR"), 
     `ClinicoPathJamoviModule`=list(
         `type`="software", 
         `author`="Serdar Balci", 

R/00jmv.R

@@ -186,7 +186,7 @@ crosstableBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Function for making Cross Tables.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # example will be added
 #'}
 #' @param data The data as a data frame.

R/crosstable.h.R

@@ -90,7 +90,7 @@ reportcatBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Function for Generating Summaries for Categorical Variables.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # example will be added
 #'}
 #' @param data the data as a data frame

R/reportcat.h.R

@@ -86,7 +86,7 @@ summarydataBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Function for Generating Summaries for Continuous Variables.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # example will be added
 #'}
 #' @param data The data as a data frame.

R/summarydata.h.R

@@ -132,7 +132,7 @@ tableoneBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Function for making Table One.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' data('histopathology')
 #' dat <- as.data.frame(histopathology)
 #' ClinicoPath::tableone(

R/tableone.h.R

@@ -259,7 +259,6 @@ vartreeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     active = list(
         todo = function() private$.items[["todo"]],
         text1 = function() private$.items[["text1"]],
-        r_cleaneddata = function() private$.items[["r_cleaneddata"]],
         text2 = function() private$.items[["text2"]]),
     private = list(),
     public=list(
@@ -281,10 +280,6 @@ vartreeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 title="Variable Tree",
                 clearWith=list(
                     "maxwidth")))
-            self$add(jmvcore::Preformatted$new(
-                options=options,
-                name="r_cleaneddata",
-                title="Cleaned Data"))
             self$add(jmvcore::Preformatted$new(
                 options=options,
                 name="text2",
@@ -317,7 +312,7 @@ vartreeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Function for Generating Tree Summaries of Variables.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # example will be added
 #'}
 #' @param data The data as a data frame.
@@ -351,7 +346,6 @@ vartreeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$text1} \tab \tab \tab \tab \tab a html \cr
-#'   \code{results$r_cleaneddata} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
 #' }
 #'

R/vartree.h.R

@@ -104,7 +104,8 @@ vennResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
-        plot = function() private$.items[["plot"]]),
+        plot = function() private$.items[["plot"]],
+        plot2 = function() private$.items[["plot2"]]),
     private = list(),
     public=list(
         initialize=function(options) {
@@ -113,7 +114,6 @@ vennResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 name="",
                 title="Venn Diagram",
                 refs=list(
-                    "venn",
                     "ClinicoPathJamoviModule"),
                 clearWith=list(
                     "var1",
@@ -132,10 +132,22 @@ vennResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 options=options,
                 title="Venn Diagram",
                 name="plot",
-                width=600,
+                width=700,
                 height=450,
                 renderFun=".plot",
-                requiresData=TRUE))}))
+                requiresData=TRUE,
+                refs=list(
+                    "venn")))
+            self$add(jmvcore::Image$new(
+                options=options,
+                title="Upset Diagram",
+                name="plot2",
+                width=700,
+                height=450,
+                renderFun=".plot2",
+                requiresData=TRUE,
+                refs=list(
+                    "upset")))}))
 
 vennBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     "vennBase",
@@ -174,6 +186,7 @@ vennBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
+#'   \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
 #' }
 #'
 #' @export

R/venn.h.R

@@ -1,12 +1,12 @@
 ---
 title: Descriptives Functions for Clinicopathological Research
 name: ClinicoPathDescriptives
-version: 0.0.2.26
+version: 0.0.2.28
 jms: '1.0'
 authors:
   - Serdar Balci
 maintainer: Serdar Balci <drserdarbalci@gmail.com>
-date: '2024-01-19'
+date: '2024-11-02'
 type: R
 description: >-
   Descriptives Functions for Clinicopathological Research Descriptive functions