update

sbalci · Dec 20, 2023 · 9d0d984 · 9d0d984
1 parent 1b3c59b
commit 9d0d984
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Showing 16 changed files with 77 additions and 53 deletions.
diff --git a/R/00jmv.R b/R/00jmv.R
@@ -524,4 +524,10 @@
         `title`="Applied Survival Analysis Using R", 
         `publisher`="Springer Cham", 
         `doi`="10.1007/978-3-319-31245-3", 
-        `url`="https://link.springer.com/book/10.1007/978-3-319-31245-3"))
+        `url`="https://link.springer.com/book/10.1007/978-3-319-31245-3"), 
+    `survivalrwnahhas`=list(
+        `type`="book chapter", 
+        `author`="Ramzi W. Nahhas", 
+        `year`=2023, 
+        `title`="Chapter 7 Survival Analysis. Introduction to Regression Methods for Public Health Using R.", 
+        `url`="https://bookdown.org/rwnahhas/RMPH/survival.html"))
diff --git a/R/multisurvival.h.R b/R/multisurvival.h.R
@@ -258,6 +258,7 @@ multisurvivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
                 refs=list(
                     "multivariable",
                     "survivaltutorial",
+                    "survivalrwnahhas",
                     "ClinicoPathJamoviModule"))
             self$add(jmvcore::Html$new(
                 options=options,

diff --git a/R/singlearm.b.R b/R/singlearm.b.R
@@ -507,16 +507,14 @@ singlearmClass <- if (requireNamespace('jmvcore', quietly=TRUE)) R6::R6Class(
 
         ## Add Calculated Time to Data ----
 
-        self$results$mydataview$setContent(
-            list(
-                head(results$cleanData)
-            )
-        )
+        # self$results$mydataview$setContent(
+        #     list(
+        #         head(results$cleanData)
+        #     )
+        # )
 
 
-        if (
-          # self$options$tint &&
-            self$options$calculatedtime && self$results$calculatedtime$isNotFilled()) {
+        if ( self$options$tint && self$options$calculatedtime && self$results$calculatedtime$isNotFilled()) {
           self$results$calculatedtime$setRowNums(results$cleanData$row_names)
           self$results$calculatedtime$setValues(results$cleanData$CalculatedTime)
         }

diff --git a/R/singlearm.h.R b/R/singlearm.h.R
@@ -286,7 +286,6 @@ singlearmResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
-        mydataview = function() private$.items[["mydataview"]],
         medianSummary = function() private$.items[["medianSummary"]],
         medianTable = function() private$.items[["medianTable"]],
         survTableSummary = function() private$.items[["survTableSummary"]],
@@ -309,7 +308,8 @@ singlearmResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "survival",
                     "survminer",
                     "ClinicoPathJamoviModule",
-                    "survivaltutorial"))
+                    "survivaltutorial",
+                    "survivalrwnahhas"))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="todo",
@@ -322,10 +322,6 @@ singlearmResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "dxdate",
                     "tint",
                     "multievent")))
-            self$add(jmvcore::Preformatted$new(
-                options=options,
-                name="mydataview",
-                title="mydataview"))
             self$add(jmvcore::Preformatted$new(
                 options=options,
                 name="medianSummary",
@@ -615,7 +611,6 @@ singlearmBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
-#'   \code{results$mydataview} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$medianSummary} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$survTableSummary} \tab \tab \tab \tab \tab a preformatted \cr

diff --git a/R/survival.h.R b/R/survival.h.R
@@ -369,6 +369,7 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "survival",
                     "survminer",
                     "survivaltutorial",
+                    "survivalrwnahhas",
                     "survivalrviews",
                     "appliedsurvivalanalysisR",
                     "ClinicoPathJamoviModule"))

diff --git a/R/survivalcont.h.R b/R/survivalcont.h.R
@@ -310,7 +310,6 @@ survivalcontResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
-        mydataview = function() private$.items[["mydataview"]],
         coxSummary = function() private$.items[["coxSummary"]],
         coxTable = function() private$.items[["coxTable"]],
         tCoxtext2 = function() private$.items[["tCoxtext2"]],
@@ -340,15 +339,12 @@ survivalcontResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
                     "survminer",
                     "dichotomizing",
                     "survivaltutorial",
+                    "survivalrwnahhas",
                     "ClinicoPathJamoviModule"))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="todo",
                 title="To Do"))
-            self$add(jmvcore::Preformatted$new(
-                options=options,
-                name="mydataview",
-                title="mydataview"))
             self$add(jmvcore::Preformatted$new(
                 options=options,
                 name="coxSummary",
@@ -866,7 +862,6 @@ survivalcontBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
-#'   \code{results$mydataview} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$coxSummary} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$coxTable} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$tCoxtext2} \tab \tab \tab \tab \tab a html \cr

diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
@@ -385,13 +385,6 @@ analyses:
     menuTitle: ROC
     description: Function for ROC Analysis.
     menuSubtitle: Decision
-  - title: Graphs and Plots
-    name: statsplot2
-    ns: ClinicoPath
-    menuGroup: JJStatsPlot
-    menuSubgroup: Variable Type Based Graphs and Plots
-    menuTitle: Graphs and Plots
-    description: Function for Generating Plots and Graphs Based on Variable Types.
   - title: Time Interval
     name: timeinterval
     ns: ClinicoPath

diff --git a/jamovi/00refs.yaml b/jamovi/00refs.yaml
@@ -634,5 +634,13 @@ refs:
         doi: 10.1007/978-3-319-31245-3
         url: https://link.springer.com/book/10.1007/978-3-319-31245-3
 
+    survivalrwnahhas:
+        type: 'book chapter'
+        author: Ramzi W. Nahhas
+        year: 2023
+        title: "Chapter 7 Survival Analysis. Introduction to Regression Methods for Public Health Using R."
+        url: https://bookdown.org/rwnahhas/RMPH/survival.html
+
+
 
 ...
diff --git a/jamovi/multisurvival.r.yaml b/jamovi/multisurvival.r.yaml
@@ -276,6 +276,7 @@ items:
 refs:
     - multivariable
     - survivaltutorial
+    - survivalrwnahhas
     - ClinicoPathJamoviModule
 
     # - name: model

diff --git a/jamovi/multisurvival.u.yaml b/jamovi/multisurvival.u.yaml
@@ -119,6 +119,7 @@ children:
             children:
               - type: Output
                 name: calculatedtime
+                enable: (tint)
   - type: CollapseBox
     label: Analysis with Multiple Outcomes
     collapsed: true
@@ -150,11 +151,16 @@ children:
           - type: ComboBox
             name: analysistype
             enable: (outcome && multievent)
-      - type: LayoutBox
-        margin: large
+      - type: Label
+        label: Calculated Outcome to Data 
+        fitToGrid: true
         children:
-          - type: Output
-            name: outcomeredifened
+          - type: LayoutBox
+            margin: large
+            children:
+              - type: Output
+                name: outcomeredifened
+                enable: (outcome && multievent)
 
 
   - type: CollapseBox
@@ -177,7 +183,7 @@ children:
               - type: ComboBox
                 name: sty
                 enable: (hr)
-                
+
       - type: Label
         label: Proportional Hazards Assumption
         fitToGrid: true

diff --git a/jamovi/singlearm.r.yaml b/jamovi/singlearm.r.yaml
@@ -18,9 +18,9 @@ items:
           - multievent
 
 
-    - name:  mydataview
-      title: mydataview
-      type:  Preformatted
+    # - name:  mydataview
+    #   title: mydataview
+    #   type:  Preformatted
 
 
     - name:  medianSummary
@@ -269,6 +269,7 @@ refs:
     - survminer
     - ClinicoPathJamoviModule
     - survivaltutorial
+    - survivalrwnahhas
 
 
 ...
diff --git a/jamovi/singlearm.u.yaml b/jamovi/singlearm.u.yaml
@@ -138,12 +138,17 @@ children:
           - type: ComboBox
             name: analysistype
             enable: (outcome && multievent)
-      - type: LayoutBox
-        margin: large
+      - type: Label
+        label: Calculated Outcome to Data 
+        fitToGrid: true
         children:
-          - type: Output
-            name: outcomeredifened
-            enable: (multievent)
+          - type: LayoutBox
+            margin: large
+            children:
+              - type: Output
+                name: outcomeredifened
+                enable: (outcome && multievent)
+
   - type: CollapseBox
     label: Plots
     collapsed: true

diff --git a/jamovi/survival.r.yaml b/jamovi/survival.r.yaml
@@ -476,6 +476,7 @@ refs:
     - survival
     - survminer
     - survivaltutorial
+    - survivalrwnahhas
     - survivalrviews
     - appliedsurvivalanalysisR
     - ClinicoPathJamoviModule

diff --git a/jamovi/survival.u.yaml b/jamovi/survival.u.yaml
@@ -113,6 +113,7 @@ children:
             children:
               - type: Output
                 name: calculatedtime
+                enable: (tint)
   - type: CollapseBox
     label: Analysis with Multiple Outcomes
     collapsed: true
@@ -144,11 +145,16 @@ children:
           - type: ComboBox
             name: analysistype
             enable: (outcome && multievent)
-      - type: LayoutBox
-        margin: large
+      - type: Label
+        label: Calculated Outcome to Data 
+        fitToGrid: true
         children:
-          - type: Output
-            name: outcomeredifened
+          - type: LayoutBox
+            margin: large
+            children:
+              - type: Output
+                name: outcomeredifened
+                enable: (multievent)
 
 
   - type: CollapseBox

diff --git a/jamovi/survivalcont.r.yaml b/jamovi/survivalcont.r.yaml
@@ -14,9 +14,9 @@ items:
     #   title: mydataview2
     #   type:  Preformatted
 
-    - name:  mydataview
-      title: mydataview
-      type:  Preformatted
+    # - name:  mydataview
+    #   title: mydataview
+    #   type:  Preformatted
 
     - name:  coxSummary
       title: '`Cox Regression Summary and Table - ${contexpl}`'
@@ -478,6 +478,7 @@ refs:
     - survminer
     - dichotomizing
     - survivaltutorial
+    - survivalrwnahhas
     - ClinicoPathJamoviModule
 
 ...
diff --git a/jamovi/survivalcont.u.yaml b/jamovi/survivalcont.u.yaml
@@ -128,6 +128,7 @@ children:
             children:
               - type: Output
                 name: calculatedtime
+                enable: (tint)
   - type: CollapseBox
     label: Analysis with Multiple Outcomes
     collapsed: true
@@ -159,11 +160,16 @@ children:
           - type: ComboBox
             name: analysistype
             enable: (outcome && multievent)
-      - type: LayoutBox
-        margin: large
+      - type: Label
+        label: Calculated Outcome to Data 
+        fitToGrid: true
         children:
-          - type: Output
-            name: outcomeredifened
+          - type: LayoutBox
+            margin: large
+            children:
+              - type: Output
+                name: outcomeredifened
+                enable: (outcome && multievent)