Merge branch 'TMB' into main

.Rbuildignore

@@ -1,4 +1,8 @@
 ^\.github$
 ^\.history$
 src/agemat.tpl
-sandbox/
+^sandbox$
+^data-raw$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# 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
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1,2 +1,11 @@
 .history
 sandbox/
+ignored/
+# results created by the vignette
+*.out
+Results/
+# files created by compiling the TMB model
+*.dll
+*.o
+# files for the pkgdown website
+docs

DESCRIPTION

@@ -1,51 +1,80 @@
-Package: nwfscAgeingError
 Type: Package
-Title: Source Code for Punt et al. (2008): Ageing Error and Imprecision
-Version: 1.3.4
+Package: AgeingError
+Title: Estimating ageing error with 'TMB' from double reads
+Version: 2.0.2
 Authors@R: c(
-  person(
-    given = c("Ian", "G."),
-    family = "Taylor",
-    email = "[email protected]",
-    role = c("aut", "cre")
-    comment = c(ORCID = "0000-0001-8489-2488")
-  ),
-  person(
-    given = c("Kelli", "F."),
-    family = "Johnson",
-    role = "aut",
-    comment = c(ORCID = "0000-0002-5149-451X")
-  ),
-  person(
-    given = c("Andre", "E."),
-    family = "Punt",
-    role = "aut",
-    comment = c(ORCID = "0000-0001-8489-2488")
-  ),
-  person(
-    given = c("James", "T."),
-    family = "Thorson",
-    role = "aut",
-    comment = c(ORCID = "0000-0001-7415-1010")
-  ),
-  person(
-    given = c("Ian", "J."),
-    family = "Stewart",
-    role = "ctb"
-  ),
-  person(
-    given = c("Melissa", "A."),
-    family = "Haltuch",
-    role = "ctb",
-    comment = c(ORCID = "0000-0003-2821-1267")
+    person(c("Andre", "E."), "Punt", role = "aut",
+           comment = c(ORCID = "0000-0001-8489-2488")),
+    person(c("Kelli", "F."), "Johnson", role = "aut",
+           comment = c(ORCID = "0000-0001-9563-1937")),
+    person(c("James", "T."), "Thorson", role = c("ctb", "cph"),
+           comment = c(ORCID = "0000-0001-7415-1010")),
+    person(c("Ian", "G."), "Taylor", email = "[email protected]", 
+           role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8489-2488")),
+    person("Paul", "Burch", role = "aut",
+           comment = c(ORCID = "0000-0002-9853-462X")),
+    person(c("Ian", "J."), "Stewart", role = "ctb"),
+    person(c("Melissa", "A."), "Haltuch", role = "ctb",
+           comment = c(ORCID = "0000-0003-2821-1267"))
   )
-  )
-Description: Source code and examples for how to use double-read data to
-    estimate ageing imprecision and bias from fishery otoliths. The code
-    was developed for Punt et al. (2008) and updated in 2022.
-URL: http://github.com/pfmc-assessments/nwfscAgeingError
-BugReports: http://github.com/pfmc-assessments/nwfscAgeingError/issues
-License: GPL-2
+Description: Implements Generalized Linear Mixed Effect Models (GLMMs) using
+    'TMB' to estimate ageing error from double reads of otoliths. The original
+    analysis (Punt et al. 2008; <doi:10.1139/F08-111>) was written in `ADMB`
+    and focused on estimating imprecision and bias. The newer version of the
+    software allows for random effects using `TMB`.
+License: GPL-3
+URL: https://pfmc-assessments.github.io/AgeingError/index.html, https://pfmc-assessments.github.io/AgeingError/, http://pfmc-assessments.github.io/AgeingError/
+BugReports: https://github.com/pfmc-assessments/AgeingError/issues
+Depends:
+    R (>= 3.5.0)
+Imports:
+    assertthat,
+    cli,
+    clisymbols,
+    fs,
+    generics,
+    glmmTMB,
+    graphics,
+    lifecycle,
+    Matrix,
+    methods,
+    mgcv,
+    mvtnorm,
+    nlme,
+    rlang,
+    stats,
+    TMB (>= 1.8.0)
+Suggests:
+    dplyr,
+    effects (>= 4.0-1),
+    emmeans (>= 1.4),
+    estimability,
+    future,
+    future.apply,
+    ggeffects,
+    ggforce,
+    ggplot2,
+    knitr,
+    lme4,
+    rgdal,
+    rmarkdown,
+    sf,
+    splancs,
+    testthat,
+    tibble,
+    visreg
+LinkingTo:
+    RcppEigen,
+    TMB
+VignetteBuilder:
+    knitr
+ByteCompile: true
+Config/testthat/edition: 3
+Config/testthat/parallel: true
+Copyright: inst/COPYRIGHTS
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+LazyData: true
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+SystemRequirements: GNU make, C++17

Makefile

@@ -0,0 +1,25 @@
+PACKAGE=AgeingError
+VERSION := $(shell sed -n '/^Version: /s///p' DESCRIPTION)
+DATE := $(shell sed -n '/^Date: /s///p' DESCRIPTION)
+TARBALL=${PACKAGE}_${VERSION}.tar.gz
+ZIPFILE=${PACKAGE}_${VERSION}.zip
+
+# Allow e.g. "make R=R-devel install"
+R=R
+
+all:
+	make doc-update
+	make build-package
+	make install
+
+doc-update:
+	echo "roxygen2::roxygenize(\".\")" | $(R) --slave
+
+build-package:
+	$(R) CMD build --no-build-vignettes --no-manual .
+
+install:
+	$(R) CMD INSTALL --preclean --no-multiarch --with-keep.source .
+
+cran-check:
+	echo "devtools::check(\".\")" | $(R) --slave

NAMESPACE

@@ -1,11 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
+export(DoApplyAgeError)
 export(PlotOutputFn)
 export(RunFn)
 export(SimulatorFn)
 export(StepwiseFn)
 export(ageing_comparison)
 export(cMx)
 export(estgrowth.vb)
+export(fit)
+export(plot_output)
 export(rMx)
+export(run)
 importFrom(stats,dnorm)
+useDynLib(AgeingError, .registration = TRUE)

NEWS.md

@@ -1,3 +1,15 @@
+# AgeingError development
+
+# AgeingError 2.0.2
+* Renamed github repository, 
+
+# AgeingError 2.0.0
+
+* Changed package name to AgeingError
+* Added TMB code that is pre-compiled in the package
+* Added `run()` as a wrapper for the code provided by @puntae
+* Increased the number of examples present in the package
+
 # nwfscAgeingError 1.3.3
 
 * Added a `NEWS.md` file to track changes to the package.