will fix #73

WIP
sbalci · Dec 10, 2023 · ce9c3fb · ce9c3fb
1 parent 4fd2f6e
commit ce9c3fb
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Showing 10 changed files with 106 additions and 39 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.2.12
-Date: 2023-12-07
+Version: 0.0.2.13
+Date: 2023-12-10
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",

diff --git a/R/survival.b.R b/R/survival.b.R
@@ -9,10 +9,10 @@ survivalClass <- if (requireNamespace('jmvcore'))
         "survivalClass",
         inherit = survivalBase,
         private = list(
-            
-            
-            
-            
+
+
+
+
             .init = function() {
 
 
@@ -36,7 +36,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
                 # }
 
             }
-            
+
             ,
 
 
@@ -66,7 +66,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
 
             all_labels <- labelled::var_label(mydata)
 
-            
+
             mytime <-
                 names(all_labels)[all_labels == self$options$elapsedtime]
 
@@ -79,9 +79,9 @@ survivalClass <- if (requireNamespace('jmvcore'))
             myfudate <-
                 names(all_labels)[all_labels == self$options$fudate]
 
-            myexplanatory <- 
+            myexplanatory <-
                 names(all_labels)[all_labels == self$options$explanatory]
-            
+
             return(list(
                 "mydata_labelled" = mydata
                 , "mytime_labelled" = mytime
@@ -90,14 +90,14 @@ survivalClass <- if (requireNamespace('jmvcore'))
                 , "myfudate_labelled" = myfudate
                 , "myexplanatory_labelled" = myexplanatory
             ))
-              
+
 
             }
 
 
 
 
-            
+
             # ,
             # .todo = function() {
             #     if (
@@ -108,7 +108,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
             #              is.null(self$options$dod) &&
             #              is.null(self$options$dooc) &&
             #              is.null(self$options$awd) && is.null(self$options$awod)
-                     
+
             #          )
             #          ) ||
 
@@ -184,7 +184,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
 
                     mydata[["mytime"]] <-
                         jmvcore::toNumeric(mydata[[mytime_labelled]])
-                    
+
 
                 } else if (tint) {
                     # Time Interval ----
@@ -272,8 +272,8 @@ survivalClass <- if (requireNamespace('jmvcore'))
             # Define Outcome ----
             ,
             .definemyoutcome = function() {
-                
-                
+
+
             labelled_data <- private$.getData()
 
             mydata <- labelled_data$mydata_labelled
@@ -293,17 +293,17 @@ survivalClass <- if (requireNamespace('jmvcore'))
                 #         myexplanatory_labelled = myexplanatory_labelled
                 #     )
                 #     )
-                
-                
-                
+
+
+
                 # mydata <- mydata_labelled #self$data
 
                 contin <- c("integer", "numeric", "double")
 
                 outcomeLevel <- self$options$outcomeLevel
                 multievent <- self$options$multievent
-                
-                
+
+
                 # outcome1 <- self$options$outcome
                 # outcome1 <- self$data[[outcome1]]
                 outcome1 <- mydata[[myoutcome_labelled]]
@@ -325,7 +325,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
                         }
 
                         mydata[["myoutcome"]] <- mydata[[myoutcome_labelled]]
-                            # mydata[[self$options$outcome]] 
+                            # mydata[[self$options$outcome]]
 
                     } else if (inherits(outcome1, "factor")) {
                         mydata[["myoutcome"]] <-
@@ -425,8 +425,8 @@ survivalClass <- if (requireNamespace('jmvcore'))
                 # mydata <- self$data
 
                 # expl <- self$options$explanatory
-                
-                
+
+
                 labelled_data <- private$.getData()
 
             mydata_labelled <- labelled_data$mydata_labelled
@@ -491,7 +491,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
 
 
 
-                cleanData <- dplyr::left_join(time, outcome, by = "row_names") %>% 
+                cleanData <- dplyr::left_join(time, outcome, by = "row_names") %>%
                     dplyr::left_join(factor, by = "row_names")
                     #  %>%
                     # dplyr::select(-row_names)
@@ -556,8 +556,8 @@ survivalClass <- if (requireNamespace('jmvcore'))
                             !!name2outcome := myoutcome,
                             !!name3explanatory := myfactor
                         )
-                        
-                        
+
+
 
                 # names(cleanData) <-
                 #     c(name1time, name2outcome, name3explanatory)
@@ -971,7 +971,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
                 # Proportional Hazards Assumption ----
 
                 if (self$options$ph_cox) {
-                    
+
                     # self$results$mydataview$setContent(
                     # list(
                     #     mydata = head(mydata),
@@ -994,7 +994,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
 
 
                     mydata[[mytime]] <- jmvcore::toNumeric(mydata[[mytime]])
-                    
+
 
                                     formula <-
                     paste('survival::Surv(',
@@ -1009,14 +1009,14 @@ survivalClass <- if (requireNamespace('jmvcore'))
 
 
                     cox_model <- survival::coxph(formula, data = mydata)
-                    
+
                     zph <- survival::cox.zph(cox_model)
-                    
+
                     self$results$cox_ph$setContent(print(zph))
-                    
+
                     image7 <- self$results$plot7
                     image7$setState(zph)
-                
+
                     }
 
             }
@@ -1264,6 +1264,9 @@ survivalClass <- if (requireNamespace('jmvcore'))
                         legend = 'none',
                         break.time.by = self$options$byplot,
                         xlim = c(0, self$options$endplot),
+                        ylim = c(
+                            self$options$ybegin_plot,
+                            self$options$yend_plot),
                         title = paste0("Survival curves for ", title2),
                         subtitle = "Based on Kaplan-Meier estimates",
                         risk.table = self$options$risktable,
@@ -1332,6 +1335,9 @@ survivalClass <- if (requireNamespace('jmvcore'))
                         legend = 'none',
                         break.time.by = self$options$byplot,
                         xlim = c(0, self$options$endplot),
+                        ylim = c(
+                            self$options$ybegin_plot,
+                            self$options$yend_plot),
                         title = paste0("Cumulative Events ", title2),
                         fun = "event",
                         risk.table = self$options$risktable,
@@ -1399,6 +1405,9 @@ survivalClass <- if (requireNamespace('jmvcore'))
                         legend = 'none',
                         break.time.by = self$options$byplot,
                         xlim = c(0, self$options$endplot),
+                        ylim = c(
+                            self$options$ybegin_plot,
+                            self$options$yend_plot),
                         title = paste0("Cumulative Hazard ", title2),
                         fun = "cumhaz",
                         risk.table = self$options$risktable,
@@ -1483,7 +1492,7 @@ survivalClass <- if (requireNamespace('jmvcore'))
             # cox.zph ----
             ,
             .plot7 = function(image7, ggtheme, theme, ...) {
-                
+
                 ph_cox <- self$options$ph_cox
 
                 if (!ph_cox)

diff --git a/R/survival.h.R b/R/survival.h.R
@@ -31,6 +31,8 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             ce = FALSE,
             ch = FALSE,
             endplot = 60,
+            ybegin_plot = 0,
+            yend_plot = 1,
             byplot = 12,
             multievent = FALSE,
             ci95 = FALSE,
@@ -184,6 +186,14 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 "endplot",
                 endplot,
                 default=60)
+            private$..ybegin_plot <- jmvcore::OptionNumber$new(
+                "ybegin_plot",
+                ybegin_plot,
+                default=0)
+            private$..yend_plot <- jmvcore::OptionNumber$new(
+                "yend_plot",
+                yend_plot,
+                default=1)
             private$..byplot <- jmvcore::OptionInteger$new(
                 "byplot",
                 byplot,
@@ -234,6 +244,8 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..ce)
             self$.addOption(private$..ch)
             self$.addOption(private$..endplot)
+            self$.addOption(private$..ybegin_plot)
+            self$.addOption(private$..yend_plot)
             self$.addOption(private$..byplot)
             self$.addOption(private$..multievent)
             self$.addOption(private$..ci95)
@@ -267,6 +279,8 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ce = function() private$..ce$value,
         ch = function() private$..ch$value,
         endplot = function() private$..endplot$value,
+        ybegin_plot = function() private$..ybegin_plot$value,
+        yend_plot = function() private$..yend_plot$value,
         byplot = function() private$..byplot$value,
         multievent = function() private$..multievent$value,
         ci95 = function() private$..ci95$value,
@@ -299,6 +313,8 @@ survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..ce = NA,
         ..ch = NA,
         ..endplot = NA,
+        ..ybegin_plot = NA,
+        ..yend_plot = NA,
         ..byplot = NA,
         ..multievent = NA,
         ..ci95 = NA,
@@ -642,6 +658,8 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "sc",
                     "endplot",
                     "byplot",
+                    "ybegin_plot",
+                    "yend_plot",
                     "ci95",
                     "risktable",
                     "censored",
@@ -667,6 +685,8 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "ce",
                     "endplot",
                     "byplot",
+                    "ybegin_plot",
+                    "yend_plot",
                     "ci95",
                     "risktable",
                     "censored",
@@ -691,6 +711,8 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "ch",
                     "endplot",
                     "byplot",
+                    "ybegin_plot",
+                    "yend_plot",
                     "ci95",
                     "risktable",
                     "censored",
@@ -715,6 +737,8 @@ survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "kmunicate",
                     "endplot",
                     "byplot",
+                    "ybegin_plot",
+                    "yend_plot",
                     "explanatory",
                     "outcome",
                     "outcomeLevel",
@@ -781,6 +805,8 @@ survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param ce .
 #' @param ch .
 #' @param endplot .
+#' @param ybegin_plot .
+#' @param yend_plot .
 #' @param byplot .
 #' @param multievent .
 #' @param ci95 .
@@ -843,6 +869,8 @@ survival <- function(
     ce = FALSE,
     ch = FALSE,
     endplot = 60,
+    ybegin_plot = 0,
+    yend_plot = 1,
     byplot = 12,
     multievent = FALSE,
     ci95 = FALSE,
@@ -895,6 +923,8 @@ survival <- function(
         ce = ce,
         ch = ch,
         endplot = endplot,
+        ybegin_plot = ybegin_plot,
+        yend_plot = yend_plot,
         byplot = byplot,
         multievent = multievent,
         ci95 = ci95,

diff --git a/debug.log b/debug.log
diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
@@ -1,12 +1,12 @@
 ---
 title: Common Analysis for Clinicopathological Research
 name: ClinicoPath
-version: 0.0.2.12
+version: 0.0.2.13
 jms: '1.0'
 authors:
   - Serdar Balci
 maintainer: Serdar Balci <drserdarbalci@gmail.com>
-date: '2023-12-07'
+date: '2023-12-10'
 type: R
 description: >-
   ClinicoPath help researchers to generate natural language summaries of their

diff --git a/jamovi/survival.a.yaml b/jamovi/survival.a.yaml
@@ -208,7 +208,6 @@ options:
       default: holm
 
 
-
     - name: ph_cox
       title: Proportional Hazards Assumption
       type: Bool
@@ -242,6 +241,16 @@ options:
       type: Integer
       default: 60
 
+    - name: ybegin_plot
+      title: Start y-axis
+      type: Number
+      default: 0.00
+
+    - name: yend_plot
+      title: End y-axis
+      type: Number
+      default: 1.00
+
 
     - name: byplot
       title: Time Interval