Merge pull request #68 from ehrlinger/pkgdown-site

Add vignette for Random Forest Survival Analysis and update DESCRIPTION

Author: ehrlinger

.Rbuildignore

@@ -34,6 +34,7 @@ framed.sty
 ^doc$
 ^Meta$
 ^_pkgdown\.yml$
+^codecov\.yml$
 ^docs$
 ^pkgdown$
 ^LICENSE\.md$

.claude/settings.local.json

@@ -24,6 +24,9 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+    # R-devel may fail due to upstream packages not yet compatible with
+    # the development version of R (e.g. lazyeval PREXPR removal).
+    continue-on-error: ${{ matrix.config.r == 'devel' }}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -47,13 +50,25 @@ jobs:
           use-public-rspm: true
           rtools-version: '44'
 
+      # On R-devel, bootstrap rcmdcheck before the main lockfile install so that
+      # the check step can run even when abandoned packages (e.g. lazyeval) that
+      # use removed C symbols (PREXPR) cause pak::lockfile_install() to abort.
+      - name: Bootstrap rcmdcheck (R-devel only)
+        if: matrix.config.r == 'devel'
+        run: install.packages("rcmdcheck")
+        shell: Rscript {0}
+
+      # R-devel may fail here due to lazyeval PREXPR; rcmdcheck is pre-installed
+      # above so the check step still runs regardless.
       - uses: r-lib/actions/setup-r-dependencies@v2
+        continue-on-error: ${{ matrix.config.r == 'devel' }}
         with:
           extra-packages: any::rcmdcheck
           cache-version: 2
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        continue-on-error: ${{ matrix.config.r == 'devel' }}
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/R-CMD-check.yaml

@@ -23,6 +23,9 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+    # R-devel may fail due to upstream packages not yet compatible with
+    # the development version of R (e.g. lazyeval PREXPR removal).
+    continue-on-error: ${{ matrix.config.r == 'devel' }}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -41,10 +44,23 @@ jobs:
           use-public-rspm: true
           rtools-version: '42'
 
+      # On R-devel, bootstrap rcmdcheck before the main lockfile install so that
+      # the check step can run even when abandoned packages (e.g. lazyeval) that
+      # use removed C symbols (PREXPR) cause pak::lockfile_install() to abort.
+      - name: Bootstrap rcmdcheck (R-devel only)
+        if: matrix.config.r == 'devel'
+        run: install.packages("rcmdcheck")
+        shell: Rscript {0}
+
+      # R-devel may fail here due to lazyeval PREXPR; rcmdcheck is pre-installed
+      # above so the check step still runs regardless.
       - uses: r-lib/actions/setup-r-dependencies@v2
+        continue-on-error: ${{ matrix.config.r == 'devel' }}
         with:
           extra-packages: rcmdcheck
           cache-version: 2
 
       - uses: r-lib/actions/setup-tinytex@v2
+
       - uses: r-lib/actions/check-r-package@v2
+        continue-on-error: ${{ matrix.config.r == 'devel' }}

.github/workflows/check-standard.yaml

@@ -46,3 +46,4 @@ docs
 vignettes/ggRandomForests_files
 vignettes/ggRandomForests.html
 
+.claude

.gitignore

@@ -1,8 +1,8 @@
 Package: ggRandomForests
 Type: Package
 Title: Visually Exploring Random Forests
-Version: 2.7.0
-Date: 2026-03-25
+Version: 2.7.0.9001
+Date: 2026-03-27
 Authors@R: person("John", "Ehrlinger",  
   role = c("aut", "cre"), 
   email = "john.ehrlinger@gmail.com")
@@ -35,6 +35,8 @@ Suggests:
     rmarkdown,
     quarto,
     pkgdown,
-    pkgload
+    pkgload,
+    knitr,
+    plotly
 VignetteBuilder: quarto
 RoxygenNote: 7.3.3

DESCRIPTION

@@ -10,11 +10,16 @@ S3method(gg_rfsrc,rfsrc)
 S3method(gg_roc,default)
 S3method(gg_roc,randomForest)
 S3method(gg_roc,rfsrc)
+S3method(gg_survival,default)
+S3method(gg_survival,rfsrc)
 S3method(gg_variable,randomForest)
 S3method(gg_variable,rfsrc)
 S3method(gg_vimp,randomForest)
 S3method(gg_vimp,rfsrc)
 S3method(plot,gg_error)
+S3method(plot,gg_partial)
+S3method(plot,gg_partial_rfsrc)
+S3method(plot,gg_partialpro)
 S3method(plot,gg_rfsrc)
 S3method(plot,gg_roc)
 S3method(plot,gg_survival)

NAMESPACE

@@ -1,5 +1,53 @@
 Package: ggRandomForests
-Version: 2.7.0
+Version: 2.8.0
+
+ggRandomForests v2.8.0
+=====================
+* S3 design overhaul: `gg_partial()`, `gg_partialpro()`, and
+  `gg_partial_rfsrc()` now stamp their return values with S3 classes
+  (`gg_partial`, `gg_partialpro`, `gg_partial_rfsrc` respectively), enabling
+  `plot()` dispatch without any boilerplate.
+* Add `plot.gg_partial()`, `plot.gg_partial_rfsrc()`, and
+  `plot.gg_partialpro()` S3 methods; continuous predictors render as line
+  plots, categorical as bar charts, faceted by variable name.  Survival
+  forests produce curves over time; two-variable surface plots group by
+  `xvar2.name`.
+* Convert `gg_survival()` to an S3 generic dispatching on the class of its
+  first argument.  New `gg_survival.rfsrc()` method extracts the survival
+  response directly from the fitted forest (no separate data argument
+  needed); `gg_survival.default()` preserves the existing interface.
+* Fix `plot.gg_survival()` auto-coercion: previously called
+  `gg_survival(rfsrc_obj)` treating the forest as the `interval` string
+  argument, causing a latent crash; replaced with `inherits()` guard.
+* Deprecate `surv_partial.rfsrc()` via `.Deprecated()` with a pointer to
+  `gg_partial_rfsrc()`; all package tests updated to suppress the warning.
+* Fix `gg_partial_rfsrc()` — `make_eval_grid()` used `unlist(dplyr::select())`
+  which coerced factor columns to integer codes; now uses `newx[[xname]]` to
+  preserve column class.  Categorical detection extended to cover
+  `is.factor()` and `is.character()` in addition to the cardinality check.
+* Add guards to `gg_partial_rfsrc()`: all-NA `xval` after NA removal now
+  emits a warning and skips the variable; all-NA grouping variable (`xvar2`)
+  calls `stop()`; `n_eval` and `cat_limit` are validated as single integers
+  >= 2 near function entry.
+* Fix cyclomatic complexity across `gg_partial_rfsrc.R`: refactored into
+  eight top-level unexported helpers (`validate_scalar_int`,
+  `validate_partial_args`, `snap_partial_time`, `make_eval_grid`,
+  `call_partial_rfsrc`, `partial_one_var`, `partial_no_group`,
+  `partial_with_group`, `split_partial_result`); all functions now score
+  below the `cyclocomp_linter` limit of 20.
+* Fix `@param partial.time` documentation: "see the section above" corrected
+  to "see the section below".
+* Replace deprecated `tidyr::gather()` with `tidyr::pivot_longer()` in
+  `plot.gg_vimp()` and `plot.gg_partialpro()`.
+* Add `gg_survival.rfsrc`, `gg_survival.default`, `plot.gg_partial`,
+  `plot.gg_partial_rfsrc`, and `plot.gg_partialpro` to `NAMESPACE`; add
+  corresponding `@rdname` / `@export` roxygen tags.
+* Update tests: add `expect_s3_class()` checks for all new classes; add
+  `plot()` smoke tests for `gg_partial`, `gg_partial_rfsrc`, `gg_partialpro`;
+  add `gg_survival.rfsrc` tests for KM extraction, `by` stratification, and
+  error on non-survival forest.
+* Add `plot.gg_partial`, `plot.gg_partial_rfsrc`, and `plot.gg_partialpro`
+  to `_pkgdown.yml` reference index.
 
 ggRandomForests v2.7.0
 =====================

NEWS.md

@@ -111,5 +111,7 @@ gg_partial <- function(part_dta,
     }
   }
 
-  return(list(continuous = continuous, categorical = categorical))
+  result <- list(continuous = continuous, categorical = categorical)
+  class(result) <- "gg_partial"
+  return(result)
 }