removed old vignette name and recreated codecov

.github/workflows/test-coverage.yaml

@@ -6,14 +6,15 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
@@ -24,20 +25,27 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          token <- Sys.getenv("CODECOV_TOKEN", "")
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
-            token = if (token != "") token
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
@@ -51,9 +59,3 @@ jobs:
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
-
-      - name: Upload coverage reports to Codecov
-        uses: codecov/[email protected]
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: ropensci/eDNAjoint

DESCRIPTION

@@ -7,7 +7,7 @@ Authors@R:
     person("Ryan P.", "Kelly", role = "ctb", email="[email protected]"),
     person("Chitra M.", "Saraswati", role = "rev"),
     person("Saras M.", "Windecker", role = "rev"))
-Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://bookdown.org/abigailkeller/eDNAjoint_vignette/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
+Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
 License: GPL-3
 URL: https://github.com/ropensci/eDNAjoint, https://docs.ropensci.org/eDNAjoint/
 BugReports: https://github.com/ropensci/eDNAjoint/issues

R/detectionCalculate.R

@@ -6,7 +6,7 @@
 #' jointModel(). Detecting species presence is defined
 #' as producing at least one true positive eDNA detection or catching at least
 #' one individual. See more examples in the
-#' \href{https://bookdown.org/abigailkeller/eDNAjoint_vignette/}{Package
+#' \href{https://ednajoint.netlify.app/}{Package
 #' Vignette}.
 #'
 #' @srrstats {G1.4} Roxygen function documentation begins here

R/detectionPlot.R

@@ -6,7 +6,7 @@
 #' jointModel(). Detecting species presence is defined as producing
 #' at least one true positive eDNA detection or catching at least one
 #' individual. See more examples in the
-#' \href{https://bookdown.org/abigailkeller/eDNAjoint_vignette/}{Package
+#' \href{https://ednajoint.netlify.app/}{Package
 #' Vignette}.
 #'
 #' @srrstats {G1.4} Roxygen function documentation begins here