Aariq · Aariq · Jul 29, 2025 · Jul 29, 2025 · Jul 29, 2025 · Jul 29, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -4,7 +4,6 @@
 ^notes$
 
 ^codecov\.yml$
-^LICENSE$
 ^LICENSE\.md$
 ^\.Rhistory$
 .github

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,14 +1,13 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -20,63 +19,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'devel'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      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 }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v3
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,29 +1,62 @@
+# 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:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
 
-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:
-          r-version: 'release'
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "bumbl" in publications use:'
 type: software
 license: CC-BY-4.0
 title: 'bumbl: Tools for Modeling Bumblebee Colony Growth and Decline'
-version: 1.0.3
+version: 1.0.4
 doi: 10.5281/zenodo.4545782
 abstract: Bumblebee colonies grow during worker production, then decline after switching
   to production of reproductive individuals (drones and gynes). This package provides
@@ -31,7 +31,7 @@ preferred-citation:
   year: '2021'
   publisher:
     name: Zenodo
-  version: 1.0.3
+  version: 1.0.4
   doi: 10.5281/zenodo.4545782
   url: https://doi.org/10.5281/zenodo.4545782
 repository: https://CRAN.R-project.org/package=bumbl

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,39 +1,42 @@
 Package: bumbl
 Title: Tools for Modeling Bumblebee Colony Growth and Decline
 Version: 1.0.3.9000
-Authors@R: c(
-    person(given = c("Eric", "R."),
-           family = "Scott",
-           role = c("aut", "cre"),
-           email = "scottericr@gmail.com",
+Authors@R: 
+    person(c("Eric", "R."), "Scott", , "scottericr@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7430-7879"))
-           )
-Description: Bumblebee colonies grow during worker production, then decline after switching to production of reproductive individuals (drones and gynes).  This package provides tools for modeling and visualizing this pattern by identifying a switchpoint with a growth rate before and a decline rate after the switchpoint. The mathematical models fit by bumbl are described in Crone and Williams (2016) <doi:10.1111/ele.12581>.
+Description: Bumblebee colonies grow during worker production, then
+    decline after switching to production of reproductive individuals
+    (drones and gynes).  This package provides tools for modeling and
+    visualizing this pattern by identifying a switchpoint with a growth
+    rate before and a decline rate after the switchpoint. The mathematical
+    models fit by bumbl are described in Crone and Williams (2016)
+    <doi:10.1111/ele.12581>.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
 URL: https://github.com/Aariq/bumbl
 BugReports: https://github.com/Aariq/bumbl/issues
 Depends:
     R (>= 3.0)
-Suggests: 
-    testthat (>= 2.1.0),
-    knitr,
-    rmarkdown,
-    covr,
-    car,
-    rsq
 Imports: 
-    dplyr,
-    rlang,
-    tidyr (>= 1.0.0),
-    purrr,
     broom,
+    dplyr,
+    ggplot2,
     glue,
+    lifecycle,
     MASS,
-    ggplot2,
-    lifecycle
-RoxygenNote: 7.2.3
-Roxygen: list(markdown = TRUE)
-VignetteBuilder: knitr
+    purrr,
+    rlang,
+    tidyr (>= 1.0.0)
+Suggests: 
+    car,
+    covr,
+    knitr,
+    rmarkdown,
+    rsq,
+    testthat (>= 2.1.0)
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2025
 COPYRIGHT HOLDER: bumbl authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 bumbl authors
+Copyright (c) 2025 bumbl authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 # bumbl (development version)
 
 - bumbl is now licenced under an MIT license
+- fixed link in documentation for `brkpt()`
 
 # bumbl 1.0.3
 

diff --git a/R/colony-growth.R b/R/colony-growth.R
@@ -13,7 +13,7 @@
 #' @param tau_optim_maxit passed to `optim()` which is used to find the optimal
 #'   change point, tau.  Mostly used for testing purposes (to force convergence
 #'   errors), but could be increased if optimal switchpoint doesn't converge.
-#' @param ... additional arguments passed to [glm()] or [glm.nb()]
+#' @param ... additional arguments passed to [glm()] or [MASS::glm.nb()]
 #' @return a tibble with a column for the winning tau and a column for the
 #'   winning model
 #' @seealso [bumbl()]

diff --git a/README.Rmd b/README.Rmd
@@ -17,13 +17,16 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-[![R build status](https://github.com/Aariq/bumbl/workflows/R-CMD-check/badge.svg)](https://github.com/Aariq/bumbl/actions) [![codecov](https://codecov.io/gh/Aariq/bumbl/branch/master/graph/badge.svg?token=SU9rm3O2cc)](https://app.codecov.io/gh/Aariq/bumbl) [![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
- [![CRAN status](https://www.r-pkg.org/badges/version/bumbl)](https://CRAN.R-project.org/package=bumbl)
+[![R-CMD-check](https://github.com/Aariq/bumbl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Aariq/bumbl/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/Aariq/bumbl/graph/badge.svg)](https://app.codecov.io/gh/Aariq/bumbl)
+[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
+[![CRAN status](https://www.r-pkg.org/badges/version/bumbl)](https://CRAN.R-project.org/package=bumbl)
 [![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/bumbl)](https://cran.r-project.org/package=bumbl)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4545782.svg)](https://doi.org/10.5281/zenodo.4545782)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4545782.svg)](https://doi.org/10.5281/zenodo.4545782) 
 
 <!-- badges: end -->
 
+
 `bumbl` implements a model for bumblebee colony growth described in Crone and Williams 2016^1^.
 It models colony growth as having a switchpoint at some time, *tau*, where the colony switches from growth and worker production to gyne production and decline.
 Currently `bumbl()` works by fitting a separate switchpoint model to each colony, optimizing the switchpoint, *tau*.
@@ -33,7 +36,7 @@ Stay tuned for future developments that may allow estimating a single value of a
 
 ## Contributing
 
-I'm looking for collaborators who know (or are willing to let me teach them) how to use git and GitHub and who have an interest in helping to develop and maintain this package long-term.
+I'm looking for collaborators who know (or are willing to let me teach them) how to use git and GitHub and who have an interest in taking over as maintainer of this package.
 I'm not a bumblebee biologist, so I would especially love a collaborator who works on bumblebees or other organisms with a similar growth, switch, decline lifecycle.
 
 I also welcome contributions including bug-fixes, improvement of documentation, additional features, or new functions relating to bumblebee ecology and demography from anyone!

diff --git a/README.md b/README.md
@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-[![R build
-status](https://github.com/Aariq/bumbl/workflows/R-CMD-check/badge.svg)](https://github.com/Aariq/bumbl/actions)
-[![codecov](https://codecov.io/gh/Aariq/bumbl/branch/master/graph/badge.svg?token=SU9rm3O2cc)](https://app.codecov.io/gh/Aariq/bumbl)
+[![R-CMD-check](https://github.com/Aariq/bumbl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Aariq/bumbl/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/Aariq/bumbl/graph/badge.svg)](https://app.codecov.io/gh/Aariq/bumbl)
 [![Project Status: Inactive – The project has reached a stable, usable
 state but is no longer being actively developed; support/maintenance
 will be provided as time
@@ -36,11 +36,10 @@ rates and *tau* for each colony.
 ## Contributing
 
 I’m looking for collaborators who know (or are willing to let me teach
-them) how to use git and GitHub and who have an interest in helping to
-develop and maintain this package long-term. I’m not a bumblebee
-biologist, so I would especially love a collaborator who works on
-bumblebees or other organisms with a similar growth, switch, decline
-lifecycle.
+them) how to use git and GitHub and who have an interest in taking over
+as maintainer of this package. I’m not a bumblebee biologist, so I would
+especially love a collaborator who works on bumblebees or other
+organisms with a similar growth, switch, decline lifecycle.
 
 I also welcome contributions including bug-fixes, improvement of
 documentation, additional features, or new functions relating to
@@ -102,15 +101,15 @@ View the `bomubs` dataset
 ``` r
 head(bombus)
 #> # A tibble: 6 × 10
-#>   site  colony  wild habitat date        week  mass d.mass floral_reso…¹ cum_f…²
-#>   <fct> <fct>  <dbl> <fct>   <date>     <int> <dbl>  <dbl>         <dbl>   <dbl>
-#> 1 PUT2  9       0.98 W       2003-04-03     0 1910.    0.1         27.8     27.8
-#> 2 PUT2  9       0.98 W       2003-04-09     1 1940    30.6         27.8     55.5
-#> 3 PUT2  9       0.98 W       2003-04-15     2 1938    28.6         27.8     83.3
-#> 4 PUT2  9       0.98 W       2003-04-22     3 1976.   67.1         27.8    111. 
-#> 5 PUT2  9       0.98 W       2003-05-01     4 2010.  101.           7.96   119. 
-#> 6 PUT2  9       0.98 W       2003-05-07     5 2143   234.           7.96   127. 
-#> # … with abbreviated variable names ¹floral_resources, ²cum_floral
+#>   site  colony  wild habitat date        week  mass d.mass floral_resources
+#>   <fct> <fct>  <dbl> <fct>   <date>     <int> <dbl>  <dbl>            <dbl>
+#> 1 PUT2  9       0.98 W       2003-04-03     0 1910.    0.1            27.8 
+#> 2 PUT2  9       0.98 W       2003-04-09     1 1940    30.6            27.8 
+#> 3 PUT2  9       0.98 W       2003-04-15     2 1938    28.6            27.8 
+#> 4 PUT2  9       0.98 W       2003-04-22     3 1976.   67.1            27.8 
+#> 5 PUT2  9       0.98 W       2003-05-01     4 2010.  101.              7.96
+#> 6 PUT2  9       0.98 W       2003-05-07     5 2143   234.              7.96
+#> # ℹ 1 more variable: cum_floral <dbl>
 ```
 
 ### Example use