v0.0.33 for jamovi library

Add parametric and tree options to survival analyses
Introduces parametric survival modeling options (flexsurv, distribution selection, splines, extrapolation, diagnostics, and plots) to the survival module. Adds decision tree (survival tree) options to multivariable survival analysis. Enhances odds ratio analysis with Firth penalized regression and user-specified positive predictor level. Updates documentation, version numbers, and jamovi module metadata accordingly.

Author: sbalci

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: jsurvival
 Title: Survival Module of ClinicoPath for jamovi
-Version: 0.0.32.64
-Date: 2025-12-31
+Version: 0.0.33
+Date: 2026-01-17
 Authors@R: person(given = "Serdar", family = "Balci", role = c("aut",
         "cre"), email = "serdarbalci@serdarbalci.com", comment =
         c(ORCID = "0000-0002-7852-3851"))

R/datetimeconverter.h.R

@@ -482,7 +482,7 @@ datetimeconverterBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
             super$initialize(
                 package = "jsurvival",
                 name = "datetimeconverter",
-                version = c(0,0,32),
+                version = c(0,0,33),
                 options = options,
                 results = datetimeconverterResults$new(options=options),
                 data = data,
@@ -504,7 +504,7 @@ datetimeconverterBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
 #' creating time-based variables.
 #'
 #' @examples
-#' # Basic datetime conversion: '0.0.32'
+#' # Basic datetime conversion: '0.0.33'
 #' datetimeconverter(
 #'   data = study_data,
 #'   datetime_var = "event_date",

R/multisurvival.b.R

@@ -8142,5 +8142,50 @@ where 0.5 suggests no discriminative ability and 1.0 indicates perfect discrimin
           })
         }
 
-    )  # Close private list
+    ), # End of private list
+    public = list(
+        #' @description
+        #' Generate R source code for Multi-Variable Survival analysis
+        #' @return Character string with R syntax for reproducible analysis
+        asSource = function() {
+            elapsedtime <- self$options$elapsedtime
+            outcome <- self$options$outcome
+
+            if (is.null(elapsedtime) || is.null(outcome))
+                return('')
+
+            # Escape variable names that contain spaces or special characters
+            elapsedtime_escaped <- if (!is.null(elapsedtime) && !identical(make.names(elapsedtime), elapsedtime)) {
+                paste0('`', elapsedtime, '`')
+            } else {
+                elapsedtime
+            }
+
+            outcome_escaped <- if (!is.null(outcome) && !identical(make.names(outcome), outcome)) {
+                paste0('`', outcome, '`')
+            } else {
+                outcome
+            }
+
+            # Build arguments
+            elapsedtime_arg <- paste0('elapsedtime = "', elapsedtime_escaped, '"')
+            outcome_arg <- paste0('outcome = "', outcome_escaped, '"')
+
+            # Get other arguments using base helper (if available)
+            args <- ''
+            if (!is.null(private$.asArgs)) {
+                args <- private$.asArgs(incData = FALSE)
+            }
+            if (args != '')
+                args <- paste0(',\n    ', args)
+
+            # Get package name dynamically
+            pkg_name <- utils::packageName()
+            if (is.null(pkg_name)) pkg_name <- "ClinicoPath"  # fallback
+
+            # Build complete function call
+            paste0(pkg_name, '::multisurvival(\n    data = data,\n    ',
+                   elapsedtime_arg, ',\n    ', outcome_arg, args, ')')
+        }
+    ) # End of public list
 )

R/multisurvival.h.R

@@ -48,6 +48,11 @@ multisurvivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
             person_time = FALSE,
             time_intervals = "12, 36, 60",
             rate_multiplier = 100,
+            use_tree = FALSE,
+            min_node = 20,
+            complexity = 0.01,
+            max_depth = 5,
+            show_terminal_nodes = FALSE,
             showExplanations = FALSE,
             showSummaries = TRUE, ...) {
 
@@ -314,6 +319,32 @@ multisurvivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
                 "rate_multiplier",
                 rate_multiplier,
                 default=100)
+            private$..use_tree <- jmvcore::OptionBool$new(
+                "use_tree",
+                use_tree,
+                default=FALSE)
+            private$..min_node <- jmvcore::OptionInteger$new(
+                "min_node",
+                min_node,
+                min=5,
+                max=100,
+                default=20)
+            private$..complexity <- jmvcore::OptionNumber$new(
+                "complexity",
+                complexity,
+                min=0.001,
+                max=0.1,
+                default=0.01)
+            private$..max_depth <- jmvcore::OptionInteger$new(
+                "max_depth",
+                max_depth,
+                min=1,
+                max=10,
+                default=5)
+            private$..show_terminal_nodes <- jmvcore::OptionBool$new(
+                "show_terminal_nodes",
+                show_terminal_nodes,
+                default=FALSE)
             private$..showExplanations <- jmvcore::OptionBool$new(
                 "showExplanations",
                 showExplanations,
@@ -369,6 +400,11 @@ multisurvivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
             self$.addOption(private$..person_time)
             self$.addOption(private$..time_intervals)
             self$.addOption(private$..rate_multiplier)
+            self$.addOption(private$..use_tree)
+            self$.addOption(private$..min_node)
+            self$.addOption(private$..complexity)
+            self$.addOption(private$..max_depth)
+            self$.addOption(private$..show_terminal_nodes)
             self$.addOption(private$..showExplanations)
             self$.addOption(private$..showSummaries)
         }),
@@ -419,6 +455,11 @@ multisurvivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
         person_time = function() private$..person_time$value,
         time_intervals = function() private$..time_intervals$value,
         rate_multiplier = function() private$..rate_multiplier$value,
+        use_tree = function() private$..use_tree$value,
+        min_node = function() private$..min_node$value,
+        complexity = function() private$..complexity$value,
+        max_depth = function() private$..max_depth$value,
+        show_terminal_nodes = function() private$..show_terminal_nodes$value,
         showExplanations = function() private$..showExplanations$value,
         showSummaries = function() private$..showSummaries$value),
     private = list(
@@ -468,6 +509,11 @@ multisurvivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
         ..person_time = NA,
         ..time_intervals = NA,
         ..rate_multiplier = NA,
+        ..use_tree = NA,
+        ..min_node = NA,
+        ..complexity = NA,
+        ..max_depth = NA,
+        ..show_terminal_nodes = NA,
         ..showExplanations = NA,
         ..showSummaries = NA)
 )
@@ -1169,7 +1215,7 @@ multisurvivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             super$initialize(
                 package = "jsurvival",
                 name = "multisurvival",
-                version = c(0,0,32),
+                version = c(0,0,33),
                 options = options,
                 results = multisurvivalResults$new(options=options),
                 data = data,
@@ -1381,6 +1427,19 @@ multisurvivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'   60+.
 #' @param rate_multiplier Specify the multiplier for incidence rates (e.g.,
 #'   100 for rates per 100 person-years, 1000 for rates per 1000 person-years).
+#' @param use_tree If true, fits a survival decision tree to identify
+#'   subgroups with different survival outcomes. Decision trees provide an
+#'   intuitive alternative to Cox regression for identifying risk factors.
+#' @param min_node The minimum number of observations required in a terminal
+#'   node. Larger values create simpler trees that may be more generalizable but
+#'   potentially miss important subgroups.
+#' @param complexity The complexity parameter for tree pruning. Higher values
+#'   result in smaller trees. This parameter controls the trade-off between tree
+#'   size and goodness of fit.
+#' @param max_depth The maximum depth of the decision tree. Limits the
+#'   complexity of the tree to avoid overfitting.
+#' @param show_terminal_nodes If true, displays Kaplan-Meier survival curves
+#'   for each terminal node of the decision tree.
 #' @param showExplanations Display detailed explanations for each analysis
 #'   component to help interpret the statistical methods and results.
 #' @param showSummaries Display natural language summaries alongside tables
@@ -1491,6 +1550,11 @@ multisurvival <- function(
     person_time = FALSE,
     time_intervals = "12, 36, 60",
     rate_multiplier = 100,
+    use_tree = FALSE,
+    min_node = 20,
+    complexity = 0.01,
+    max_depth = 5,
+    show_terminal_nodes = FALSE,
     showExplanations = FALSE,
     showSummaries = TRUE) {
 
@@ -1564,6 +1628,11 @@ multisurvival <- function(
         person_time = person_time,
         time_intervals = time_intervals,
         rate_multiplier = rate_multiplier,
+        use_tree = use_tree,
+        min_node = min_node,
+        complexity = complexity,
+        max_depth = max_depth,
+        show_terminal_nodes = show_terminal_nodes,
         showExplanations = showExplanations,
         showSummaries = showSummaries)