Merge branch 'main' into index-split

Author: seananderson

.Rbuildignore

@@ -22,3 +22,5 @@
 ^vignettes/web_only$
 revdep/
 ^vignettes/articles$
+^doc$
+^Meta$

.github/workflows/R-CMD-check-valgrind3.yaml

@@ -0,0 +1,70 @@
+on: workflow_dispatch
+
+name: R-CMD-check-with-valgrind
+
+jobs:
+  R-CMD-check:
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # - {os: windows-latest, r: 'release'}
+          # - {os: macOS-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
+      _R_CHECK_USE_VALGRIND_: true
+      _R_CHECK_MATRIX_DATA_: true
+
+    steps:
+      - 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
+
+      - name: Install remotes
+        run: install.packages('remotes')
+        shell: Rscript {0}
+
+      - 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", "20.04.2"))')
+          sudo apt-get install --yes valgrind
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+          needs: check
+
+      - name: Check with valgrind
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: rcmdcheck::rcmdcheck(args = c("--use-valgrind", "--no-manual", "--as-cran", "--ignore-vignettes", "--no-build-vignettes"), build_args = c("--no-manual", "--no-build-vignettes"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

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

@@ -1,8 +1,6 @@
-# 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
 on:
   push:
-    branches: [main, dev, fmesher2]
+    branches: [main, dev]
   pull_request:
     branches: [main, dev]
 
@@ -26,91 +24,28 @@ jobs:
         # - {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@v2
+      - 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@v2
+      - 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 macOS
-        if: runner.os == 'macOS'
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("sf")
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("textshaping")
-          remotes::install_github("pbs-assess/sdmTMBextra")
-          install.packages("Matrix", type = "source")
-          install.packages("TMB", type = "source")
-        shell: Rscript {0}
-
-      - name: Install dependencies Ubuntu
-        if: runner.os == 'Linux'
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("knitr")
-          remotes::install_cran("rmarkdown")
-          remotes::install_cran("rcmdcheck")
-          remotes::install_github("pbs-assess/sdmTMBextra")
-          install.packages("Matrix", type = "source")
-          install.packages("TMB", type = "source")
-        shell: Rscript {0}
-
-      - name: Install dependencies Windows
-        if: runner.os == 'Windows'
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("knitr")
-          remotes::install_cran("rmarkdown")
-          remotes::install_cran("rcmdcheck")
-          remotes::install_github("pbs-assess/sdmTMBextra")
-          install.packages("Matrix", type = "source")
-          install.packages("TMB", type = "source")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--no-build-vignettes"), build_args = c("--no-manual", "--no-build-vignettes"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: |
+            any::rcmdcheck
+            any::textshaping
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - 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")'

.gitignore

@@ -18,3 +18,5 @@ README_cache/*
 Dockerfile
 revdep/
 scratch/VAST-EAO*
+tags
+Session.vim

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9013
+Version: 0.6.0.9038
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),
@@ -60,11 +60,10 @@ Copyright: inst/COPYRIGHTS
 URL: https://pbs-assess.github.io/sdmTMB/, https://github.com/pbs-assess/sdmTMB
 BugReports: https://github.com/pbs-assess/sdmTMB/issues
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.1.0)
 Imports:
     assertthat,
     abind,
-    clisymbols,
     cli,
     fmesher,
     fishMod,
@@ -95,6 +94,7 @@ Suggests:
     knitr,
     rmarkdown,
     sf,
+    spatstat.data,
     splancs,
     testthat,
     tibble,

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(cAIC,sdmTMB)
 S3method(coef,sdmTMB)
 S3method(confint,sdmTMB)
 S3method(df.residual,sdmTMB)
@@ -21,10 +22,12 @@ S3method(simulate,sdmTMB)
 S3method(summary,sdmTMB)
 S3method(terms,sdmTMB)
 S3method(tidy,sdmTMB)
+S3method(tidy,sdmTMB_cv)
 S3method(vcov,sdmTMB)
 export(Beta)
 export(add_barrier_mesh)
 export(add_utm_columns)
+export(cAIC)
 export(censored_poisson)
 export(delta_beta)
 export(delta_gamma)
@@ -38,6 +41,7 @@ export(delta_truncated_nbinom1)
 export(delta_truncated_nbinom2)
 export(dharma_residuals)
 export(extract_mcmc)
+export(gamma_cv)
 export(gamma_mix)
 export(gather_sims)
 export(gengamma)

NEWS.md

@@ -1,33 +1,91 @@
-# sdmTMB (development version)
+# sdmTMB 0.7.0
+
+## New features
+
+* Add option for random slopes, or random intercepts to be passed in in 
+  `lme4` style formulas, `density ~ (1 | fyear)` or `density ~ (depth | fyear)`,
+  Matches output of `lme4` and `glmmTMB`, and summarizes output with `tidy()`.
+
+* Add `project()` experimental function.
+
+* Add `get_eao()` to calculate effective area occupied.
+
+* Allow predicting on new data with `t2()` smoothers. #413
+
+* Add priors for `breakpt()` and `logistic()` parameters. #403
+
+* Add priors on time-varying SD parameters (`sigma_V`).
+
+* Add `cAIC()` for calculating *conditional* AIC. Theory based on
+  <https://arxiv.org/abs/2411.14185>; also see
+  <https://doi.org/10.1002/ecy.4327>. J.T. Thorson wrote the function code.
+  EDF (effective degrees of freedom) will ultimately be further split
+  (e.g., split by smoothers) and added to `summary.sdmTMB()`. #383 #387
+
+* Add EDF (effective degrees of freedom) printing to smoothers with 
+  `print.sdmTMB()` and `summary.sdmTMB()`. Set argument `edf = TRUE`.
+  E.g. `print(fit, edf = TRUE)`. #383 #387
 
 * At experimental function `get_index_split()`, which takes care of 
   splitting a prediction grid by time, undoing the prediction and 
   area-integration index calculations for each chunk to save memory.
 
-* Add `return_tmb_report` to `simulate.sdmTMB()`.
-
 * Add `newdata` argument to `simulate.sdmTMB()`. This enables simulating on
   a new data frame similar to how one would predict on new data.
 
 * Add `mle_mvn_samples` argument to `simulate.sdmTMB()`. Defaults to "single".
   If "multiple", then a sample from the random effects is taken for each
   simulation iteration.
 
-* Add `project()` experimental function.
+* Allow for specifying only lower or upper limits. #394
+
+* `sdmTMB_cv()` gains a `tidy()` and `print()` method for output. #319
+
+* `simulate.sdmTMB()` method now has an `return_tmb_report` argument.
 
-* Add print method for `sdmTMB_cv()` output. #319
+## New vignettes/articles
+
+* Add forecasting and presence-only article vignettes. See
+  <https://pbs-assess.github.io/sdmTMB/articles/>
+
+* Add vignette on multispecies models with sdmTMB (or any case where one wants
+  additional spatial and or spatiotemporal fields by some group).
+  See <https://pbs-assess.github.io/sdmTMB/articles/>
+
+## Minor improvements and fixes
+
+* Fix bug in a check in `make_mesh()` around if coordinates look
+  overly large. #427
+
+* Re-enable bias correction for `get_cog()` (get center of gravity).
+
+* Add check for `Inf`/`-Inf` values before fitting. #408
+
+* Add linear component of smoothers to `tidy()`. #90
+
+* Add time varying AR(1) correlation to `tidy()` and `print()`. #374
+
+* Warn if parameter limits are set with `newton_loops > 0`. #394
+
+* Fix bug in `est` column when predicting on new data with Poisson-link
+  delta models with `type = "link"` and `re_form = NA`. #389
+
+* Fix bug in `s95` parameter reporting from the `tidy()` method. `s95` is
+  present in the logistic threshold models. The model itself was fine but the
+  `s95` parameter was supposed to be reported by `tidy()` as a combination of two
+  other parameters. This also affected the output in `print()`/`summary()`.
 
 * Add progress bar to `simulate.sdmTMB()`. #346
 
 * Add AUC and TSS examples to cross validation vignette. #268
 
-* Add `model` (linear predictor number) argument to coef() method. Also,
+* Add `model` (linear predictor number) argument to `coef()` method. Also,
   write documentation for `?coef.sdmTMB`. #351
 
-* Add helpful error message if some coordinates in make_mesh() are NA. #365
+* Add helpful error message if some coordinates in `make_mesh()` are `NA`. #365
 
 * Add informative message if fitting with an offset but predicting with offset
-  argument left at NULL on newdata. #372
+  argument left at `NULL` on `newdata`. #372
 
 * Fix passing of `offset` argument through in `sdmTMB_cv()`. Before it was being
   omitted in the prediction (i.e., set to 0). #372
@@ -41,8 +99,10 @@
   distribution first before multiplying by the probability of a non-zero.
   Thanks to @tom-peatman #350
 
-* Add `get_eao()` to calculate effective area occupied.
-
+* Add option for `area` to be passed in as the name of a column in the 
+  data frame to be used for area weighting. Used in `get_index()`, 
+  `get_cog()`, `get_eao()`, etc.
+  
 # sdmTMB 0.6.0
 
 * Pass several arguments to `DHARMa::plotQQunif()`.