diff --git a/R/00jmv.R b/R/00jmv.R index ac52678e..1be3e573 100644 --- 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 index 4ce2beba..6187d458 100644 --- 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 index 093d9e84..c7201f7e 100644 --- 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 index 3fad8b1b..0985bcc1 100644 --- 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 index 43802b63..6931dd2a 100644 --- 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 index 241ea6e6..d1ddc8fd 100644 --- 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 index ab6afdee..78391315 100644 --- 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 index 84be55e1..a8b3109b 100644 --- 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 index b465a0d3..544454cd 100644 --- 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 index d0bc41ed..4e99dbc7 100644 --- 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 index 2dd30ef4..3b4dc678 100644 --- 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 index c03e7537..2ac8677d 100644 --- 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 index 2b916326..99d76def 100644 --- 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 index 6d173248..e098f9e5 100644 --- 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 index 072555fc..f67d8ef2 100644 --- 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 index f042ee61..750c9b29 100644 --- 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)