WIP jjstatsplot functions

sbalci · Jun 7, 2020 · f20ac2a · f20ac2a
1 parent bccf767
commit f20ac2a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -72,11 +72,6 @@ Suggests:
     gtsummary,
     vctrs,
     patchwork
-Remotes:
-    ndphillips/FFTrees,
-    easystats/report,
-    spgarbet/tangram,
-    cran/rmngb
 VignetteBuilder:
     knitr
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,7 +2,6 @@
 
 export(agreement)
 export(alluvial)
-export(bartlett_message)
 export(competingsurvival)
 export(correlation)
 export(crosstable)
@@ -11,8 +10,8 @@ export(decisioncalculator)
 export(gtsummary)
 export(icccoeff)
 export(jjbarstats)
+export(jjbarstats2)
 export(jjbetweenstats)
-export(jjcoefstats)
 export(jjcorrmat)
 export(jjdotplotstats)
 export(jjhistostats)
@@ -21,7 +20,6 @@ export(jjscatterstats)
 export(jjwithinstats)
 export(jviolin)
 export(multisurvival)
-export(normality_message)
 export(oddsratio)
 export(pairchi2)
 export(reportcat)
@@ -35,17 +33,6 @@ export(vartree)
 import(ggplot2)
 import(jmvcore)
 importFrom(R6,R6Class)
-importFrom(crayon,blue)
-importFrom(crayon,green)
-importFrom(crayon,red)
-importFrom(crayon,yellow)
 importFrom(jmvcore,toNumeric)
 importFrom(magrittr,"%>%")
-importFrom(rlang,":=")
-importFrom(rlang,as_name)
-importFrom(rlang,ensym)
-importFrom(rlang,new_formula)
-importFrom(stats,bartlett.test)
-importFrom(stats,na.omit)
-importFrom(stats,shapiro.test)
 importFrom(utils,data)
diff --git a/R/jjbarstats.b.R b/R/jjbarstats.b.R
@@ -20,8 +20,7 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 # TODO ----
 
                     todo <- glue::glue(
-                        "
-                <br>Welcome to ClinicoPath
+                "<br>Welcome to ClinicoPath
                 <br><br>
                 This tool will help you generate Bar Charts.
                 <br><br>
@@ -98,27 +97,37 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
 
 
-                mydep <- mydata[[self$options$dep]]
+                # mydep <- mydata[[self$options$dep]]
+                # mygroup <- mydata[[self$options$group]]
 
-                mygroup <- mydata[[self$options$group]]
+
+                dep <- self$options$dep
+
+                group <- self$options$group
+
+
+                dep <- jmvcore::composeTerm(components = dep)
+
+                group <- jmvcore::composeTerm(components = group)
 
 
                 # ggbarstats ----
                 # bar charts for categorical data
                 # https://indrajeetpatil.github.io/ggstatsplot/reference/ggbarstats.html
 
 
-                plotData <- data.frame(gr = mygroup,
-                                       dp = mydep)
 
+                plot <-
+                    ggstatsplot::ggbarstats(
+                    data = mydata,
+                    main = !!dep,
+                    condition = !!group,
+
+                    paired = paired,
 
-                plot <- ggstatsplot::ggbarstats(data = plotData,
-                                                main = dp,
-                                                condition = gr,
 
                     counts = NULL,
                     ratio = NULL,
-                    paired = paired,
                     results.subtitle = TRUE,
                     sample.size.label = TRUE,
                     label = "percentage",
@@ -171,10 +180,22 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
     # Prepare Data ----
 
+    mydata <- self$data
+
 
+    # direction, paired ----
 
-    mydata <- self$data
+    direction <- self$options$direction
+
+    if (direction == "repeated") {
+
+        paired <- TRUE
+
+    } else if (direction == "independent") {
 
+        paired <- FALSE
+
+    }
 
     # Exclude NA ----
 
@@ -184,33 +205,36 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
 
 
-    mydep <- mydata[[self$options$dep]]
+    dep <- self$options$dep
+
+    group <- self$options$group
+
+
+    dep <- jmvcore::composeTerm(components = dep)
+
+    group <- jmvcore::composeTerm(components = group)
+
+
 
-    mygroup <- mydata[[self$options$group]]
 
     # grouped_ggbarstats ----
     # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggbarstats.html
 
 
 
     if ( !is.null(self$options$grvar) ) {
-        mygrvar <- mydata[[self$options$grvar]]
-    }
-
+        grvar <- self$options$grvar
 
-    if ( !is.null(self$options$grvar) ) {
+        plot2 <- ggstatsplot::grouped_ggbarstats(
+            data = mydata,
+            main = !!dep,
+            condition = !!group,
+            grouping.var = !!grvar,
 
-        plotData <- data.frame(gr = mygroup,
-                               dp = mydep,
-                               grvar = mygrvar)
+            paired = paired,
 
 
-        plot2 <- ggstatsplot::grouped_ggbarstats(
-            data = plotData,
-            main = dp,
-            condition = gr,
             counts = NULL,
-            grouping.var = grvar,
             title.prefix = NULL,
             output = "plot",
             x = NULL,

diff --git a/R/jjbarstats.h.R b/R/jjbarstats.h.R
@@ -78,8 +78,8 @@ jjbarstatsResults <- if (requireNamespace('jmvcore')) R6::R6Class(
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
-        plot = function() private$.items[["plot"]],
-        plot2 = function() private$.items[["plot2"]]),
+        plot2 = function() private$.items[["plot2"]],
+        plot = function() private$.items[["plot"]]),
     private = list(),
     public=list(
         initialize=function(options) {
@@ -101,31 +101,31 @@ jjbarstatsResults <- if (requireNamespace('jmvcore')) R6::R6Class(
                     "direction")))
             self$add(jmvcore::Image$new(
                 options=options,
-                name="plot",
-                title="`Bar Chart ${group} - {dep}`",
+                name="plot2",
+                title="`Bar Chart ${group} - {dep} by {grvar}`",
                 width=800,
                 height=600,
-                renderFun=".plot",
+                renderFun=".plot2",
                 requiresData=TRUE,
                 clearWith=list(
                     "dep",
                     "group",
                     "grvar",
-                    "direction")))
+                    "direction"),
+                visible="(grvar)"))
             self$add(jmvcore::Image$new(
                 options=options,
-                name="plot2",
-                title="`Bar Chart ${group} - {dep} by {grvar}`",
+                name="plot",
+                title="`Bar Chart ${group} - {dep}`",
                 width=800,
                 height=600,
-                renderFun=".plot2",
+                renderFun=".plot",
                 requiresData=TRUE,
                 clearWith=list(
                     "dep",
                     "group",
                     "grvar",
-                    "direction"),
-                visible="(grvar)"))}))
+                    "direction")))}))
 
 jjbarstatsBase <- if (requireNamespace('jmvcore')) R6::R6Class(
     "jjbarstatsBase",
@@ -166,8 +166,8 @@ jjbarstatsBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' @return A results object containing:
 #' \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$plot2} \tab \tab \tab \tab \tab an image \cr
+#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
 #' }
 #'
 #' @export