v0.0.32

Author: sbalci

.claude/commands/update-refs.md

@@ -41,7 +41,7 @@ jamovi/00refs.yaml
 1. **Detect packages in `.b.R`**
    - Scan for `library()`, `require()`, and `pkg::` usage.
    - Extract unique package names.
-   - **Filter out foundational packages**: Excludes `jmvcore`, `ggplot2`, `R6`, `stats`, `utils`, `kableExtra`, `rlang`, `dplyr`, `tidyr` from individual function refs.
+   - **Filter out foundational packages**: Excludes `jmvcore`, `ggplot2`, `R6`, `stats`, `utils`, `kableExtra`, `rlang`, `dplyr`, `tidyr`, `glue`, `stringr`, `htmltools`, `labelled`, `scales`, `purrr`, `gt`, `DiagrammeRsvg`, `base`, `RColorBrewer`, `gridExtra`, `tibble`, `tidyr`, `grDevices`, `grid` from individual function refs.
 
 2. **Ensure package refs exist in `jamovi/00refs.yaml`**
    - Check whether each package is already listed under `refs:`.

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Comprehensive Analysis for Clinicopathological Research
-Version: 0.0.31.87
-Date: 2025-10-08
+Version: 0.0.32
+Date: 2025-10-09
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",

R/00jmv.R

@@ -1081,13 +1081,13 @@
         `title`="geepack: R package", 
         `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=geepack", 
         `url`="https://CRAN.R-project.org/package=geepack"), 
-    `urvival`=list(
+    `survival`=list(
         `type`="software", 
         `author`=NULL, 
         `year`=NULL, 
-        `title`="urvival: R package", 
-        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=urvival", 
-        `url`="https://CRAN.R-project.org/package=urvival"), 
+        `title`="survival: R package", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=survival", 
+        `url`="https://CRAN.R-project.org/package=survival"), 
     `party`=list(
         `type`="software", 
         `author`=NULL, 

R/conditionalinference.h.R

@@ -248,7 +248,7 @@ conditionalinferenceResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6
                     "Strobl2007",
                     "Survival",
                     "ClinicoPathJamoviModule",
-                    "urvival",
+                    "survival",
                     "party"))
             self$add(jmvcore::Html$new(
                 options=options,

R/curemodels.h.R

@@ -177,7 +177,7 @@ curemodelsResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 title="Cure Models for Long-term Survivors",
                 refs=list(
                     "ClinicoPathJamoviModule",
-                    "urvival",
+                    "survival",
                     "parallel",
                     "smcure",
                     "flexsurvcure",

R/extratrees.h.R

@@ -339,7 +339,7 @@ extratreesResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "ranger",
                     "randomForestSRC",
                     "ClinicoPathJamoviModule",
-                    "urvival"))
+                    "survival"))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="todo",

R/gradientboosting.h.R

@@ -310,7 +310,7 @@ gradientboostingResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6
                     "gbm",
                     "xgboost",
                     "ClinicoPathJamoviModule",
-                    "urvival",
+                    "survival",
                     "Matrix"))
             self$add(jmvcore::Html$new(
                 options=options,

R/patientsimilarity.h.R

@@ -266,7 +266,7 @@ patientsimilarityResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R
                     "ClinicoPathJamoviModule",
                     "Rtsne",
                     "umap",
-                    "urvival",
+                    "survival",
                     "urvminer",
                     "dbscan",
                     "cluster",

R/stagemigration.h.R

@@ -2396,7 +2396,7 @@ stagemigrationResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                     "ggplot2",
                     "timeROC",
                     "dcurves",
-                    "urvival",
+                    "survival",
                     "viridis",
                     "gridExtra",
                     "coxme",

R/stagemigration1.h.R

@@ -563,7 +563,7 @@ stagemigration1Results <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C
                     "ggplot2",
                     "timeROC",
                     "dcurves",
-                    "urvival",
+                    "survival",
                     "viridis",
                     "gridExtra",
                     "coxme",