better frequency table per discussion #3

sbalci · Apr 19, 2023 · 667997d · 667997d
1 parent bcbffba
commit 667997d
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diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: meddecide
 Title: Functions for Medical Decision Making in ClinicoPath jamovi Module
-Version: 0.0.2.07
-Date: 2022-09-20
+Version: 0.0.2.08
+Date: 2023-04-19
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -37,4 +37,4 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/R/agreement.b.R b/R/agreement.b.R
@@ -150,6 +150,29 @@ agreementClass <- if (requireNamespace("jmvcore")) R6::R6Class("agreementClass",
             self$results$text$setContent(result)
 
 
+
+            result3 <- ratings %>%
+                dplyr::group_by_all() %>%
+                dplyr::count() %>%
+                as.data.frame() %>%
+                htmlTable::htmlTable()
+
+            self$results$text2$setContent(result3)
+
+
+
+            # freqtable <- self$results$freqtable
+            #
+            # data_frame <- result3
+            # for (i in seq_along(data_frame[, 1, drop = T])) {
+            #     freqtable$addRow(rowKey = i, values = c(data_frame[i,]))
+            # }
+
+
+
+
+
+
             result1 <- irr::agree(ratings)
 
             # self$results$text1$setContent(result1[["value"]])

diff --git a/R/agreement.h.R b/R/agreement.h.R
@@ -63,8 +63,9 @@ agreementResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     "agreementResults",
     inherit = jmvcore::Group,
     active = list(
-        text = function() private$.items[["text"]],
-        irrtable = function() private$.items[["irrtable"]]),
+        irrtable = function() private$.items[["irrtable"]],
+        text2 = function() private$.items[["text2"]],
+        text = function() private$.items[["text"]]),
     private = list(),
     public=list(
         initialize=function(options) {
@@ -76,15 +77,6 @@ agreementResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "irr",
                     "PathologyKappa",
                     "ClinicoPathJamoviModule"))
-            self$add(jmvcore::Preformatted$new(
-                options=options,
-                name="text",
-                title="Table",
-                visible="(sft)",
-                clearWith=list(
-                    "vars",
-                    "wght",
-                    "exct")))
             self$add(jmvcore::Table$new(
                 options=options,
                 name="irrtable",
@@ -121,6 +113,24 @@ agreementResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                         `title`="p-value", 
                         `type`="number", 
                         `format`="zto,pvalue")),
+                clearWith=list(
+                    "vars",
+                    "wght",
+                    "exct")))
+            self$add(jmvcore::Html$new(
+                options=options,
+                name="text2",
+                title="Table",
+                visible="(sft)",
+                clearWith=list(
+                    "vars",
+                    "wght",
+                    "exct")))
+            self$add(jmvcore::Preformatted$new(
+                options=options,
+                name="text",
+                title="Table",
+                visible="(sft)",
                 clearWith=list(
                     "vars",
                     "wght",
@@ -168,8 +178,9 @@ agreementBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'   than 3 observers.
 #' @return A results object containing:
 #' \tabular{llllll}{
-#'   \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$irrtable} \tab \tab \tab \tab \tab a table \cr
+#'   \code{results$text2} \tab \tab \tab \tab \tab a html \cr
+#'   \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr
 #' }
 #'
 #' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:

diff --git a/R/decision.b.R b/R/decision.b.R
@@ -1,7 +1,4 @@
 #' @title Medical Decision Making
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 #'

diff --git a/R/decisioncalculator.b.R b/R/decisioncalculator.b.R
@@ -1,8 +1,4 @@
 #' @title Decision Calculator
-#'
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 #' @importFrom utils data

diff --git a/R/kappasizeci.b.R b/R/kappasizeci.b.R
@@ -1,7 +1,4 @@
 #' @title Confidence Interval Approach for the Number of Subjects Required
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 

diff --git a/R/kappasizefixedn.b.R b/R/kappasizefixedn.b.R
@@ -1,7 +1,4 @@
 #' @title Lowest Expected Value for a fixed sample size
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 

diff --git a/R/kappasizepower.b.R b/R/kappasizepower.b.R
@@ -1,7 +1,4 @@
 #' @title Power Approach for the Number of Subjects Required
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 

diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
@@ -1,12 +1,12 @@
 ---
 title: Functions for Medical Decision in ClinicoPath jamovi Module
 name: meddecide
-version: 0.0.2.07
+version: 0.0.2.08
 jms: '1.0'
 authors:
   - Serdar Balci
 maintainer: Serdar Balci <drserdarbalci@gmail.com>
-date: '2022-06-14'
+date: '2023-04-19'
 type: R
 description: |-
   This module contains functions for interobserver and intraobserver reliability

diff --git a/jamovi/agreement.a.yaml b/jamovi/agreement.a.yaml
@@ -33,7 +33,7 @@ options:
 
 
     - name: sft
-      title: Frequency Table
+      title: Frequency Tables
       type: Bool
       default: false
       description:

diff --git a/jamovi/agreement.r.yaml b/jamovi/agreement.r.yaml
@@ -11,16 +11,6 @@ items:
     #   clearWith:
     #       - vars
 
-    - name:  text
-      title: 'Table'
-      type:  Preformatted
-      visible: (sft)
-      clearWith:
-          - vars
-          - wght
-          - exct
-
-
     # - name: result_cohen
     #   title: 'result_cohen'
     #   type: Preformatted
@@ -97,6 +87,48 @@ items:
           - wght
           - exct
 
+
+    - name:  text2
+      title: 'Table'
+      type:  Html
+      visible: (sft)
+      clearWith:
+          - vars
+          - wght
+          - exct
+
+
+    - name:  text
+      title: 'Table'
+      type:  Preformatted
+      visible: (sft)
+      clearWith:
+          - vars
+          - wght
+          - exct
+
+
+
+
+
+    # - name:  freqtable
+    #   title: 'Frequency Table'
+    #   type: Table
+    #   columns:
+    #     - name: values
+    #       title: 'Values'
+    #       type: text
+    #   clearWith:
+    #       - vars
+    #       - wght
+    #       - exct
+
+
+
+
+
+
+
 refs:
     - irr
     - PathologyKappa

diff --git a/man/agreement.Rd b/man/agreement.Rd
diff --git a/man/agreementClass.Rd b/man/agreementClass.Rd