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sbalci · Jul 4, 2020 · b4d7eba · b4d7eba
1 parent fa63637
commit b4d7eba
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Showing 10 changed files with 22 additions and 70 deletions.
diff --git a/R/jjbarstats.h.R b/R/jjbarstats.h.R
@@ -8,8 +8,6 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
         initialize = function(
             dep = NULL,
             group = NULL,
-            grvar = NULL,
-            counts = NULL,
             excl = TRUE, ...) {
 
             super$initialize(
@@ -34,43 +32,22 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                     "nominal"),
                 permitted=list(
                     "factor"))
-            private$..grvar <- jmvcore::OptionVariable$new(
-                "grvar",
-                grvar,
-                suggested=list(
-                    "ordinal",
-                    "nominal"),
-                permitted=list(
-                    "factor"))
-            private$..counts <- jmvcore::OptionVariable$new(
-                "counts",
-                counts,
-                suggested=list(
-                    "continuous"),
-                permitted=list(
-                    "numeric"))
             private$..excl <- jmvcore::OptionBool$new(
                 "excl",
                 excl,
                 default=TRUE)
 
             self$.addOption(private$..dep)
             self$.addOption(private$..group)
-            self$.addOption(private$..grvar)
-            self$.addOption(private$..counts)
             self$.addOption(private$..excl)
         }),
     active = list(
         dep = function() private$..dep$value,
         group = function() private$..group$value,
-        grvar = function() private$..grvar$value,
-        counts = function() private$..counts$value,
         excl = function() private$..excl$value),
     private = list(
         ..dep = NA,
         ..group = NA,
-        ..grvar = NA,
-        ..counts = NA,
         ..excl = NA)
 )
 
@@ -145,8 +122,6 @@ jjbarstatsBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' @param data The data as a data frame.
 #' @param dep .
 #' @param group .
-#' @param grvar .
-#' @param counts .
 #' @param excl .
 #' @return A results object containing:
 #' \tabular{llllll}{
@@ -159,34 +134,25 @@ jjbarstats <- function(
     data,
     dep,
     group,
-    grvar,
-    counts,
     excl = TRUE) {
 
     if ( ! requireNamespace('jmvcore'))
         stop('jjbarstats requires jmvcore to be installed (restart may be required)')
 
     if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep))
     if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group))
-    if ( ! missing(grvar)) grvar <- jmvcore::resolveQuo(jmvcore::enquo(grvar))
-    if ( ! missing(counts)) counts <- jmvcore::resolveQuo(jmvcore::enquo(counts))
     if (missing(data))
         data <- jmvcore::marshalData(
             parent.frame(),
             `if`( ! missing(dep), dep, NULL),
-            `if`( ! missing(group), group, NULL),
-            `if`( ! missing(grvar), grvar, NULL),
-            `if`( ! missing(counts), counts, NULL))
+            `if`( ! missing(group), group, NULL))
 
     for (v in dep) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
     for (v in group) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
-    for (v in grvar) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
 
     options <- jjbarstatsOptions$new(
         dep = dep,
         group = group,
-        grvar = grvar,
-        counts = counts,
         excl = excl)
 
     analysis <- jjbarstatsClass$new(

diff --git a/R/jjwithinstats.b.R b/R/jjwithinstats.b.R
@@ -21,7 +21,7 @@ jjwithinstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 todo <- glue::glue(
                 "<br>Welcome to ClinicoPath
                 <br><br>
-                This tool will help you generate Bar Charts.
+                This tool will help you generate Violin Plots for repeated measurements.
                 <br><br>
                 This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggwithinstats.html' target='_blank'>ggwithinstats</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggwithinstats.html' target='_blank'>grouped_ggwithinstats</a>.
                 <br>

diff --git a/R/jjwithinstats.h.R b/R/jjwithinstats.h.R
@@ -74,7 +74,7 @@ jjwithinstatsResults <- if (requireNamespace('jmvcore')) R6::R6Class(
             super$initialize(
                 options=options,
                 name="",
-                title="Violin Plots to Compare Between Groups",
+                title="Violin Plots to Compare Within Groups",
                 refs=list(
                     "ggplot2",
                     "ggstatsplot"))
@@ -135,7 +135,7 @@ jjwithinstatsBase <- if (requireNamespace('jmvcore')) R6::R6Class(
                 requiresMissings = FALSE)
         }))
 
-#' Violin Plots to Compare Between Groups
+#' Violin Plots to Compare Within Groups
 #'
 #' 
 #'

diff --git a/data/histopathologyGraphsPlots.omv b/data/histopathologyGraphsPlots.omv
diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
@@ -64,13 +64,13 @@ analyses:
     menuSubgroup: Continious vs Continious
     menuTitle: Scatter Plot
     menuSubtitle: Scatter Plot
-  - title: Violin Plots to Compare Between Groups
+  - title: Violin Plots to Compare Within Groups
     name: jjwithinstats
     ns: jjstatsplot
     menuGroup: JJStatsPlot
     menuSubgroup: Categorical vs Numeric
-    menuTitle: Violin Plots to Compare Between Groups
-    menuSubtitle: Categorical vs Numeric
+    menuTitle: Violin Plots to Compare Within Groups
+    menuSubtitle: Repeated Measurements
   - title: Graphs and Plots
     name: statsplot2
     ns: jjstatsplot

diff --git a/jamovi/jjbarstats.a.yaml b/jamovi/jjbarstats.a.yaml
@@ -37,17 +37,17 @@ options:
       suggested: [ ordinal, nominal ]
       permitted: [ factor ]
 
-    - name: grvar
-      title: 'Split by: (Optional)'
-      type: Variable
-      suggested: [ ordinal, nominal ]
-      permitted: [ factor ]
-
-    - name: counts
-      title: 'Counts: (Optional)'
-      type: Variable
-      suggested: [ continuous ]
-      permitted: [ numeric ]
+    # - name: grvar
+    #   title: 'Split by: (Optional)'
+    #   type: Variable
+    #   suggested: [ ordinal, nominal ]
+    #   permitted: [ factor ]
+
+    # - name: counts
+    #   title: 'Counts: (Optional)'
+    #   type: Variable
+    #   suggested: [ continuous ]
+    #   permitted: [ numeric ]
 
 
     # - name: direction

diff --git a/jamovi/jjbarstats.u.yaml b/jamovi/jjbarstats.u.yaml
@@ -21,20 +21,6 @@ children:
             name: group
             maxItemCount: 1
             isTarget: true
-      - type: TargetLayoutBox
-        label: 'Split by: (Optional)'
-        children:
-          - type: VariablesListBox
-            name: grvar
-            maxItemCount: 1
-            isTarget: true
-      - type: TargetLayoutBox
-        label: 'Counts: (Optional)'
-        children:
-          - type: VariablesListBox
-            name: counts
-            maxItemCount: 1
-            isTarget: true
   - type: LayoutBox
     margin: large
     children:

diff --git a/jamovi/jjwithinstats.a.yaml b/jamovi/jjwithinstats.a.yaml
@@ -1,9 +1,9 @@
 ---
 name:  jjwithinstats
-title: Violin Plots to Compare Between Groups
+title: Violin Plots to Compare Within Groups
 menuGroup: JJStatsPlot
 menuSubgroup: Categorical vs Numeric
-menuSubtitle: Categorical vs Numeric
+menuSubtitle: Repeated Measurements
 version: '1.0.0'
 jas: '1.2'
 

diff --git a/jamovi/jjwithinstats.r.yaml b/jamovi/jjwithinstats.r.yaml
@@ -1,6 +1,6 @@
 ---
 name:  jjwithinstats
-title: Violin Plots to Compare Between Groups
+title: Violin Plots to Compare Within Groups
 jrs:   '1.1'
 
 items:

diff --git a/jamovi/jjwithinstats.u.yaml b/jamovi/jjwithinstats.u.yaml
@@ -1,4 +1,4 @@
-title: Violin Plots to Compare Between Groups
+title: Violin Plots to Compare Within Groups
 name: jjwithinstats
 jus: '3.0'
 stage: 0