Penultimate PR before version 2

CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md

@@ -59,7 +59,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at .github/. 
+reported to the community leaders responsible for enforcement at [email protected]. 
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

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

@@ -1,14 +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, dev]
+    branches: [main, master]
   pull_request:
-    branches: [main, dev]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -23,19 +25,20 @@ jobs:
 
           - {os: windows-latest, r: 'release'}
           # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          - {os: windows-latest, r: 'oldrel-3'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
 
     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
 
@@ -53,3 +56,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/paper.yaml

@@ -21,7 +21,7 @@ jobs:
           journal: joss
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           path: paper/paper.pdf

.github/workflows/pkgdown.yaml

@@ -2,14 +2,16 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-    branches: main
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ 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/test-coverage.yaml

@@ -2,49 +2,60 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-    branches: main
+    branches: [main, master, dev]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: macos-latest
+    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:
           use-public-rspm: true
 
       - 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: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            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: true
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - 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

.gitignore

@@ -10,9 +10,8 @@
 
 *.html
 
-docs/
-inst/docs/
-inst/doc
-paper/paper.pdf
-scripts/boron_samples1
-scripts/checks.md
+/docs/
+/inst/docs/
+/paper/paper.pdf
+/scripts/boron_samples1
+/scripts/checks.md

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ssdtools
 Title: Species Sensitivity Distributions
-Version: 1.0.6.9016
+Version: 1.0.6.9018
 Authors@R: c(
     person("Joe", "Thorley", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7683-4592")),
@@ -15,9 +15,7 @@ Authors@R: c(
     person("Doug", "Spry", role = "ctb"),
     person("Rick", "van Dam", role = "ctb"),
     person("Graham", "Batley", role = "ctb"),
-    person("Yulia", "Cuthbertson", role = "ctb"),
     person("Tony", "Bigwood", role = "ctb"),
-    person("Michael", "Antenucci", role = "ctb"),
     person("Ali", "Azizishirazi", role = "ctb"),
     person("Nadine", "Hussein", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0003-4470-8361")),
@@ -38,9 +36,9 @@ Description: Species sensitivity distributions are cumulative probability
     different species as described by Posthuma et al.(2001)
     <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
     fit distributions such as the gamma, log-logistic, log-normal and
-    log-normal log-normal mixture. Multiple distributions can
-    be averaged using Akaike Information Criteria.  Confidence intervals
-    on hazard concentrations and proportions are produced by parametric
+    log-normal log-normal mixture. Multiple distributions can be averaged
+    using Akaike Information Criteria.  Confidence intervals on hazard
+    concentrations and proportions are produced by parametric
     bootstrapping.
 License: Apache License (== 2.0) | file LICENSE
 URL: https://github.com/bcgov/ssdtools, https://bcgov.github.io/ssdtools/
@@ -53,6 +51,7 @@ Imports:
     furrr,
     generics,
     ggplot2,
+    glue,
     goftest,
     graphics,
     grid,
@@ -61,6 +60,7 @@ Imports:
     plyr,
     purrr,
     Rcpp,
+    rlang,
     scales,
     ssddata,
     stats,
@@ -69,7 +69,7 @@ Imports:
     TMB,
     universals,
     utils,
-    VGAM
+    withr
 Suggests:
     actuar,
     covr,
@@ -80,22 +80,21 @@ Suggests:
     fitdistrplus,
     foreach,
     future,
-    glue,
     grDevices,
     knitr,
+    latex2exp,
     magrittr,
     mle.tools,
     patchwork,
     R.rsp,
     readr,
     reshape2,
-    rlang,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     tidyr,
     tidyselect,
     tinytex,
-    withr
+    VGAM
 LinkingTo: 
     Rcpp,
     RcppEigen,

NAMESPACE

@@ -58,6 +58,7 @@ export(is_censored)
 export(logLik)
 export(nobs)
 export(npars)
+export(params)
 export(pgompertz)
 export(plgumbel)
 export(plot)
@@ -68,6 +69,7 @@ export(rgompertz)
 export(rlgumbel)
 export(scale_color_ssd)
 export(scale_colour_ssd)
+export(ssd_censor_data)
 export(ssd_data)
 export(ssd_dists)
 export(ssd_dists_all)
@@ -96,6 +98,7 @@ export(ssd_hc_burrlioz)
 export(ssd_hp)
 export(ssd_hp_bcanz)
 export(ssd_is_censored)
+export(ssd_label_comma)
 export(ssd_licensing_md)
 export(ssd_match_moments)
 export(ssd_min_pmix)
@@ -145,11 +148,10 @@ export(tidy)
 export(waiver)
 import(chk)
 import(ggplot2)
+import(rlang)
 importFrom(Rcpp,sourceCpp)
 importFrom(TMB,MakeADFun)
 importFrom(TMB,sdreport)
-importFrom(VGAM,gompertz)
-importFrom(VGAM,vglm)
 importFrom(abind,abind)
 importFrom(furrr,furrr_options)
 importFrom(furrr,future_map)
@@ -159,6 +161,7 @@ importFrom(generics,tidy)
 importFrom(ggplot2,autoplot)
 importFrom(ggplot2,sym)
 importFrom(ggplot2,waiver)
+importFrom(glue,glue)
 importFrom(goftest,ad.test)
 importFrom(goftest,cvm.test)
 importFrom(graphics,par)
@@ -173,15 +176,16 @@ importFrom(grid,segmentsGrob)
 importFrom(lifecycle,deprecate_soft)
 importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
+importFrom(lifecycle,deprecated)
+importFrom(lifecycle,expect_defunct)
 importFrom(lifecycle,expect_deprecated)
 importFrom(parallel,nextRNGStream)
 importFrom(parallel,nextRNGSubStream)
 importFrom(plyr,summarise)
 importFrom(purrr,list_assign)
 importFrom(purrr,transpose)
-importFrom(scales,comma)
+importFrom(scales,label_percent)
 importFrom(scales,manual_pal)
-importFrom(scales,percent)
 importFrom(scales,trans_breaks)
 importFrom(ssddata,gm_mean)
 importFrom(stats,coef)

NEWS.md

@@ -1,6 +1,6 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
-# ssdtools 1.0.6.9016
+# ssdtools 1.0.6.9018
 
 ## Additions
 
@@ -11,14 +11,20 @@
   - `samples` argument to include bootstrap samples as list of numeric vector(s).
   - `save_to` argument to specify a directory in which to save the bootstrap datasets as csv files and parameter estimates as rds files. The files are named `data_000000001_xx.csv` and `estimates_000000001_xx.rds` etc where `xx` is the distribution. The parent data set and estimates are named `boot_000000000_xx.csv` and `estimates_000000000_xx.csv`.
 - Added `ssd_hp_bcanz()` and `ssd_hp.fitburrlioz()` function to get hazard proportions.
+- Added `ssd_label_comma()` for x-axis labels.
 - Added `trans = "log10"` and `add_x = 0` arguments to `ssd_plot()` and `ssd_plot_data()`.
 - Added `ssd_pmulti()`, `ssd_qmulti()` and `ssd_rmulti()` for combined mixture distributions.
 - Added `ssd_exx()` functions to get default parameter estimates for distributions.
+- Added `ssd_censor_data()` to censor data. 
 - Added David Fox and Rebecca Fisher as co-authors.
 - Added `npars` argument to `ssd_dists_bcanz()`.
+- Added `big.mark = ","` for x-axis labels and `suffix = "%"` to y-axis labels to plotting functions.
 
 ## Modifications
 
+- Only non-parametric bootstrap for censored data.
+- Changed `at_boundary_ok = TRUE` to ensure `lnorm_lnorm` mixture distribution included.
+- Changed `computable = TRUE` to as not required for bootstrapping.
 - Changed to `min_pboot = 0.95` for all functions.
 - Changed `min_pmix = 0` to `min_pmix = ssd_min_pmix(nrow(data))` to by default 
 give set min_pmix to be `0.1` or `3/nrow(data)` if greater to improve convergence of mixture models.
@@ -43,11 +49,13 @@ give set min_pmix to be `0.1` or `3/nrow(data)` if greater to improve convergenc
 
 ## Deprecation
 
+- Soft-deprecated `comma_signif()`.
 - Soft-deprecated argument `percent = 5` for `proportion = 0.05` for `ssd_hc()` and `predict()`.
-- `is_censored()`, `ssd_plot_cf()` and `comma_signif(...)` now warn deprecated unconditionally.
-- `plot.fitdists()` now defunct.
-- Removed defunct `ssd_cfplot()`
+- `is_censored()`, `plot.fitdists()`, `ssd_plot_cf()` `geom_ssd()`, `stat_ssd()`, `xgompertz()`, `xlgumbel`, `ssd_hc_burrlioz()` now defunct.
+- Deprecated `ssd_wqg_bc()` and `ssd_wqg_burrlioz()`. (#75).
+- Deprecated `ssd_fit_bcanz()` and `ssd_hp_bcanz()`.
 - Removed `ccme_data` and `ccme_boron` data set.
+- Removed `pearson1000` data set (now in `ssdtests` data).
 
 # ssdtools 1.0.6
 
@@ -91,7 +99,7 @@ ssdtools version 1.0.0 is the first major release of `ssdtools` with some import
 
 ## Fitting
 
-An important change to the functionality of `ssd_fit_dists()` was to switch from model fitting using [`fitdistrplus`](https://github.com/aursiber/fitdistrplus) to [`TMB`](https://github.com/kaskr/adcomp) which has resulted in improved handling of censored data.
+An important change to the functionality of `ssd_fit_dists()` was to switch from model fitting using [`fitdistrplus`](https://github.com/lbbe-software/fitdistrplus) to [`TMB`](https://github.com/kaskr/adcomp) which has resulted in improved handling of censored data.
 Although it was hoped that model fitting would be faster this is currently not the case.
 
 As a result of the change the `fitdists` objects returned by `ssd_fit_dists()` from previous versions of `ssdtools` are not compatible with the major release and should be regenerated.