Merge pull request #74 from brandmaier/merging_tbrick_boruta

merging tbrick changes

.Rbuildignore

@@ -13,3 +13,7 @@ Makefile
 ^pkgdown$
 ^LICENSE\.md$
 ^\.travis\.yml$
+misc
+cran-comments.md
+^CRAN-SUBMISSION$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,29 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-Win
+
+jobs:
+  R-CMD-check:
+    runs-on: windows-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

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

@@ -0,0 +1,29 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/R-devel-check.yml

@@ -0,0 +1,17 @@
+# check package on latest R devel version
+#
+on: workflow-dispatch
+
+name: R-CMD-check
+
+jobs:
+  devel-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 'devel' 
+        # Use "renv" to retrieve R version recorded in renv.lock file.
+    - run: 'R CMD build ./'    
+    - run: 'R CMD check semtree*.tar.gz'

.github/workflows/R-tests.yml

@@ -0,0 +1,31 @@
+on:
+   workflow_dispatch 
+
+name: Tests
+
+jobs:
+  document:
+    name: run tests
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          extra-packages: |
+            any::testthat
+            any::devtools
+#          needs: pr-document
+      - name: install package
+        run: devtools::install_github("brandmaier/semtree")
+        shell: Rscript {0}
+
+      - name: run test
+        run: testthat::test_dir("tests/testthat/")
+        shell: Rscript {0}

.github/workflows/test-coverage.yml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -5,4 +5,9 @@
 inst/doc
 doc
 Meta
+/doc/
+/Meta/
+cran_comments.md
+CRAN*
 .DS_Store
+

DESCRIPTION

@@ -11,15 +11,10 @@ Depends:
     R (>= 2.10),
     OpenMx (>= 2.6.9),
 Imports:
-    bitops,
-    sets,
-    digest,
     rpart,
     rpart.plot (>= 3.0.6),
-    plotrix,
-    cluster,
-    stringr,
     lavaan,
+    cluster,
     ggplot2,
     tidyr,
     methods,
@@ -30,7 +25,6 @@ Imports:
     clisymbols,
     future.apply,
     data.table,
-    ctsemOMX,
     expm,
     gridBase
 Suggests:
@@ -39,7 +33,9 @@ Suggests:
     viridis,
     MASS,
     psychTools,
-    testthat
+    testthat,
+    future,
+    ctsemOMX
 Description: SEM Trees and SEM Forests -- an extension of model-based decision
     trees and forests to Structural Equation Models (SEM). SEM trees hierarchically
     split empirical data into homogeneous groups each sharing similar data patterns
@@ -53,9 +49,10 @@ Description: SEM Trees and SEM Forests -- an extension of model-based decision
 License: GPL-3
 Encoding: UTF-8
 LazyLoad: yes
-Version: 0.9.19
-Date: 2023-03-03
-RoxygenNote: 7.3.1
+Version: 0.9.20
+Date: 2024-03-25
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 BugReports: https://github.com/brandmaier/semtree/issues
 URL: https://github.com/brandmaier/semtree
+Language: en-US

NAMESPACE

@@ -26,11 +26,13 @@ S3method(print,summary.semtree)
 S3method(proximity,semforest)
 S3method(proximity,semforest_node_id)
 S3method(proximity,semforest_stripped)
+S3method(prune,semforest)
 S3method(prune,semtree)
 S3method(strip,semforest)
 S3method(strip,semtree)
 S3method(summary,semforest)
 S3method(summary,semtree)
+S3method(toLatex,semtree)
 export(biodiversity)
 export(boruta)
 export(diversityMatrix)
@@ -59,10 +61,12 @@ export(prune)
 export(se)
 export(semforest)
 export(semforest.control)
+export(semforest_control)
 export(semforest_score_control)
 export(semtree)
 export(semtree.constraints)
 export(semtree.control)
+export(semtree_control)
 export(strip)
 export(subforest)
 export(subtree)
@@ -72,7 +76,6 @@ export(varimpConvergencePlot)
 import(OpenMx)
 import(data.table)
 import(rpart)
-importFrom(bitops,bitAnd)
 importFrom(data.table,data.table)
 importFrom(grDevices,heat.colors)
 importFrom(graphics,barplot)
@@ -92,7 +95,6 @@ importFrom(methods,is)
 importFrom(parallel,clusterMap)
 importFrom(parallel,parLapply)
 importFrom(sandwich,bread)
-importFrom(sets,as.set)
 importFrom(stats,as.dist)
 importFrom(stats,as.formula)
 importFrom(stats,cmdscale)

NEWS.md

@@ -1,12 +1,20 @@
-# semtree 0.9.20 (2023)
+# semtree 0.9.20 (2024)
 
-- changed default behavior of print function of varimp, such that na.omit=TRUE,
- which is consistent with other packages like party or partykit
+- added an error handler for score-based tests when the vcov matrix cannot be computed (e.g., models with Heywood cases)
+- leaner package imports: removed dependency on bitops and stringr package
+- prefer `semforest_control()` over `semforest.control()` and `semtree_control()` over `semtree.control()`
+- added heuristics for choosing `mtry` in forests (if `NULL`) and for choosing `min.N` and `min.bucket` (if `NULL`)
+- moved dependency on `ctsemOMX` to suggested package
 
-# semtree 0.9.19 (2022)
+# semtree 0.9.19 (2023)
 
+- changed default behavior of print function of `varimp`, such that na.omit=TRUE, which is consistent with other packages like party or partykit
+- fixed issues with `toTable()`-command, by default, all parameters are shown now, also fixed a bug with score-based tests and toTable()
+- fixed problem with focus-parameters and variable importance
 - bugfix in score-based tests that sometimes did not respect min.N constraints
 - new functionality for parameter contribution evaluation
+- more verbose vignettes
+- removed dependency on set, plotrix and digest package to make package imports leaner
 
 # semtree 0.9.18 (2022)
 
@@ -65,6 +73,6 @@
 - deprecated partialDependencePlot and introduced partialDependence() function with S3 plotting method
 - added parallel computation option to partialDependence
 - added new demo scripts
-- added extra.legend paramter to varimpConvergencePlot
+- added extra.legend parameter to varimpConvergencePlot
 - bugfix in traverse() that led to underestimations of variable importance in some cases
 - added error message when trying to use lavaan and global constraints

R/OpenMx_scores_input.R

@@ -5,6 +5,25 @@ OpenMx_scores_input <- function(x, control) {
   p_star <- p * (p + 1) / 2
   p_star_means <- p * (p + 3) / 2
 
+  # AB: give pseudo-labels to matrices if
+  # unlabelled parameters are given
+  candidate_param_id <- which(startsWith(x=names(x$output$estimate), prefix=x$name))
+  if (length(candidate_param_id)>0) {
+    for (k in candidate_param_id) {
+      candidate_param_name <- names(x$output$estimate)[k]
+      cplen <- nchar(x$name)
+      candidate_matrix <- substr(candidate_param_name, cplen+2,cplen+2)
+      candidate_pos <- as.integer(strsplit(substr(candidate_param_name, cplen+4, nchar(candidate_param_name)-1),",")[[1]])
+      if (candidate_matrix=="A") {
+        x$A$labels[candidate_pos[1], candidate_pos[2]]<-candidate_param_name        
+      } else if (candidate_matrix=="S") {
+        x$S$labels[candidate_pos[1], candidate_pos[2]]<-candidate_param_name        
+      } else if (candidate_matrix == "M") {
+        x$M$labels[candidate_pos]<-candidate_param_name        
+      }
+    }
+  }
+
   if (control$linear | imxHasDefinitionVariable(x)) {
 
     param_names <- names(x$output$estimate)

R/aggregateVarimp.R

@@ -1,4 +1,3 @@
-
 aggregateVarimp <-
   function(vimp,
            aggregate = "mean",