Merge pull request #51 from wjakethompson/doc-cleanup

Clean up documentation

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

@@ -1,10 +1,13 @@
+# 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
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -16,25 +19,24 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'release', rtools: ''}
-          - {os: windows-latest, r: 'release', rtools: '43'}
-          - {os: ubuntu-latest, r: 'devel', rtools: '', http-user-agent: 'release'}
-          - {os: ubuntu-latest, r: 'release', rtools: ''}
-          - {os: ubuntu-latest, r: 'oldrel-1', rtools: ''}
+          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          rtools-version: ${{ matrix.config.rtools }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
           extra-repositories: https://mc-stan.org/r-packages/
@@ -57,3 +59,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -1,19 +1,21 @@
+# 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: lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pkgdown.yaml

@@ -1,13 +1,16 @@
+# 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]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -17,9 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -43,7 +47,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -1,8 +1,12 @@
+# 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:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -11,9 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -22,7 +27,6 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -50,9 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -1,19 +1,22 @@
+# 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
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -25,6 +28,7 @@ jobs:
           cache-version: 3
           extra-packages: |
             any::covr
+            any::xml2
             github::stan-dev/cmdstanr
           upgrade: 'TRUE'
           needs: coverage
@@ -37,7 +41,7 @@ jobs:
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             line_exclusions = list("src/stanExports_gqs_loglik.h",
@@ -50,6 +54,15 @@ jobs:
           )
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
@@ -59,7 +72,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.github/workflows/update-citation-cff.yaml

@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -64,11 +64,13 @@ Suggests:
     testthat (>= 3.0.0)
 Additional_repositories: https://mc-stan.org/r-packages/
 Config/testthat/edition: 3
-Config/Needs/website: wjakethompson/wjake, showtext, ggdist, english
+Config/Needs/website: r-dcm/rdcmtemplate, wjakethompson/wjake, showtext, ggdist, english
+Config/Needs/documentation: openpharma/roxylint
+Config/roxylint: list(linters = roxylint::tidy)	
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE)
+Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "roxylint::roxylint"))
 RoxygenNote: 7.3.2
 Biarch: true
 SystemRequirements: GNU make

R/data.R

@@ -1,6 +1,7 @@
-#' Examination for the Certificate of Proficiency in English (ECPE)
+#' Examination for the Certificate of Proficiency in English
 #'
-#' This is data from the grammar section of the ECPE, administered annually by
+#' This is data from the grammar section of the Examination for the Certificate
+#' of Proficiency in English (\acronym{ECPE}), administered annually by
 #' the English Language Institute at the University of Michigan. This data
 #' contains responses to 28 questions from 2,922 respondents, which ask
 #' respondents to complete a sentence with the correct word. This data set has
@@ -21,6 +22,8 @@
 #' * `resp_id`: Respondent identifier
 #' * `E1`-`E28`: Dichotomous item responses to the 28 ECPE items
 #'
+#' @concept Examination for the Certificate of Proficiency in English
+#'
 #' @references Buck, G., & Tatsuoka, K. K. (1998). Application of the rule-space
 #'   procedure to language testing: Examining attributes of a free response
 #'   listening test. *Language Testing, 15*(2), 119-157.
@@ -52,7 +55,7 @@
 "ecpe_qmatrix"
 
 
-#' MacReady & Dayton (1977) Multiplication Data
+#' MacReady & Dayton (1977) multiplication data
 #'
 #' This is a small data set of multiplication item responses. This data contains
 #' responses to 4 items from 142 respondents, which ask respondents to complete
@@ -64,6 +67,9 @@
 #' * `respondent`: Respondent identifier
 #' * `mdm1`-`mdm4`: Dichotomous item responses to the 4 multiplication items
 #'
+#' @concept MacReady
+#' @concept Dayton
+#'
 #' @references MacReady, G. B., & Dayton, C. M. (1977). The use of probabilistic
 #'   models in the assessment of mastery. *Journal of Educational Statistics,
 #'   2*(2), 99-120. \doi{10.2307/1164802}

R/discrimination.R

@@ -1,10 +1,10 @@
 #' Item, attribute, and test-level discrimination indices
 #'
-#' The cognitive diagnostic index (CDI) is a measure of how well an assessment
-#' is able to distinguish between attribute profiles. The index was originally
-#' proposed by Henson & Douglas (2005) for item- and test-level discrimination,
-#' and then expanded by Henson et al. (2008) to include attribute-level
-#' discrimination indices.
+#' The cognitive diagnostic index (\acronym{CDI}) is a measure of how well an
+#' assessment is able to distinguish between attribute profiles.
+#' The index was originally proposed by Henson & Douglas (2005) for item- and
+#' test-level discrimination, and then expanded by Henson et al. (2008) to
+#' include attribute-level discrimination indices.
 #'
 #' @param model The estimated model to be evaluated.
 #' @param weight_prevalence Logical indicating whether the discrimination
@@ -29,9 +29,11 @@
 #'
 #' @return A list with two elements:
 #'   * `item_discrimination`: A [tibble][tibble::tibble-package] with one row
-#'     per item containing the CDI for the item and any relevant attributes.
+#'     per item containing the \acronym{CDI} for the item and any relevant
+#'     attributes.
 #'   * `test_discrimination`: A [tibble][tibble::tibble-package] with one row
-#'     containing the total CDI for the assessment and for each attribute.
+#'     containing the total \acronym{CDI} for the assessment and for each
+#'     attribute.
 #' @export
 #'
 #' @references Henson, R., & Douglas, J. (2005). Test construction for cognitive

R/extract.R

@@ -1,4 +1,4 @@
-#' Extract components of a `measrfit` object.
+#' Extract components of a `measrfit` object
 #'
 #' @param model The estimated to extract information from.
 #' @param ... Additional arguments passed to specific methods.
@@ -18,8 +18,8 @@ measr_extract <- function(model, ...) {
 #'     For `what = "odds_ratio_flags"` and
 #'     `what = "conditional_prob_flags"`, the compatibility interval used for
 #'     determining model fit flags to return. For example, a `ppmc_interval` of
-#'     0.95 (the default) will return any PPMCs where the posterior predictive
-#'     *p*-value (ppp) is less than 0.025 or greater than 0.975.
+#'     0.95 (the default) will return any \acronym{PPMC}s where the posterior
+#'     predictive *p*-value (ppp) is less than 0.025 or greater than 0.975.
 #'
 #'   * `agreement`:
 #'
@@ -100,6 +100,11 @@ measr_extract <- function(model, ...) {
 #'     Reliability information must first be added to the model using
 #'     [add_reliability()].
 #'
+#' @concept Sinharay
+#' @concept Goodman
+#' @concept Templin
+#' @concept Bradshaw
+#'
 #' @return The extracted information. The specific structure will vary depending
 #'   on what is being extracted, but usually the returned object is a
 #'   [tibble][tibble::tibble-package] with the requested information.