Merge pull request #27 from nimble-dev/AD-rc0

AD support
nimble-dev · Jun 25, 2024 · 6f62c31 · 6f62c31
2 parents 383047e + 6ed4f42
commit 6f62c31
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -9,10 +9,12 @@ on:
     branches:
       - main
       - master
+      - AD-rc0
   pull_request:
     branches:
       - main
       - master
+      - AD-rc0
 
 name: R-CMD-check
 
@@ -27,11 +29,11 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}#, http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-latest,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          # - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          # - {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -41,12 +43,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -70,10 +72,16 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
+          sudo apt-get install libcurl4-openssl-dev  # needed for R pkg curl -> covr
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+          # install.packages('devtools')
+          # install.packages('pracma')
+          # install.packages('numDeriv')
+          #  devtools::install_github("nimble-dev/nimble", ref = "ADoak", subdir = "packages/nimble") # Remove this line once AD is released in NIMBLE
         shell: Rscript {0}
 
       - name: Session info

diff --git a/.github/workflows/check_windows.yaml b/.github/workflows/check_windows.yaml
@@ -9,10 +9,12 @@ on:
     branches:
       - main
       - master
+      - AD-rc0
   pull_request:
     branches:
       - main
       - master
+      - AD-rc0
 
 name: R-CMD-check
 
@@ -37,12 +39,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -70,6 +72,10 @@ jobs:
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+#          install.packages('devtools')
+#          install.packages('pracma')
+#          install.packages('numDeriv')
+#          devtools::install_github("nimble-dev/nimble", ref = "ADoak", subdir = "packages/nimble") # Remove this line once AD is released in NIMBLE
         shell: Rscript {0}
 
       - name: Session info

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,21 @@
 Package: nimbleEcology
 Type: Package
 Title: Distributions for Ecological Models in 'nimble'
-Version: 0.4.1
+Version: 0.5.0
 Maintainer: Benjamin R. Goldstein <[email protected]>
 Authors@R: c(person("Benjamin R.", "Goldstein", role = c("aut", "cre"),
-                     email = "ben.goldstein@berkeley.edu"),
+                     email = "bgoldst2@ncsu.edu"),
               person("Daniel", "Turek", role = "aut"),
               person("Lauren", "Ponisio", role = "aut"),
+              person("Wei", "Zhang", role = "ctb"),
               person("Perry", "de Valpine", role = "aut"))
-Date: 2021-11-1
+Date: 2024-06-24
 Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. 
   Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models.
   (Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
 License: GPL-3
-Copyright: Copyright (c) 2019, Perry de Valpine, Ben Goldstein, Daniel Turek, Lauren Ponisio
-Depends: R (>= 3.4.0), nimble
+Copyright: Copyright (c) 2024, Perry de Valpine, Ben Goldstein, Daniel Turek, Lauren Ponisio
+Depends: R (>= 4.0.0), nimble
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/nimble-dev/nimbleEcology
@@ -27,8 +28,9 @@ Collate:
   dHMM.R
   dOcc.R
   dNmixture.R
+  dNmixtureAD.R
   zzz.R
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Suggests: 
     rmarkdown,
     knitr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,7 @@
+# Generated by roxygen2: do not edit by hand
 
+export(dBetaBinom_s)
+export(dBetaBinom_v)
 export(dCJS_ss)
 export(dCJS_sv)
 export(dCJS_vs)
@@ -19,19 +22,38 @@ export(dDynOcc_vvs)
 export(dDynOcc_vvv)
 export(dHMM)
 export(dHMMo)
-export(dNmixture_s)
-export(dNmixture_v)
-export(dNmixture_BNB_oneObs)
-export(dNmixture_BNB_v)
-export(dNmixture_BNB_s)
-export(dNmixture_BBP_oneObs)
-export(dNmixture_BBP_v)
-export(dNmixture_BBP_s)
+export(dNmixtureAD_BBNB_oneObs)
+export(dNmixtureAD_BBNB_s)
+export(dNmixtureAD_BBNB_v)
+export(dNmixtureAD_BBP_oneObs)
+export(dNmixtureAD_BBP_s)
+export(dNmixtureAD_BBP_v)
+export(dNmixtureAD_BNB_oneObs)
+export(dNmixtureAD_BNB_s)
+export(dNmixtureAD_BNB_v)
+export(dNmixtureAD_s)
+export(dNmixtureAD_v)
 export(dNmixture_BBNB_oneObs)
-export(dNmixture_BBNB_v)
 export(dNmixture_BBNB_s)
+export(dNmixture_BBNB_steps)
+export(dNmixture_BBNB_v)
+export(dNmixture_BBP_oneObs)
+export(dNmixture_BBP_s)
+export(dNmixture_BBP_steps)
+export(dNmixture_BBP_v)
+export(dNmixture_BNB_oneObs)
+export(dNmixture_BNB_s)
+export(dNmixture_BNB_steps)
+export(dNmixture_BNB_v)
+export(dNmixture_s)
+export(dNmixture_steps)
+export(dNmixture_v)
 export(dOcc_s)
 export(dOcc_v)
+export(nimBetaFun)
+export(nimNmixPois_logFac)
+export(rBetaBinom_s)
+export(rBetaBinom_v)
 export(rCJS_ss)
 export(rCJS_sv)
 export(rCJS_vs)
@@ -52,27 +74,38 @@ export(rDynOcc_vvs)
 export(rDynOcc_vvv)
 export(rHMM)
 export(rHMMo)
-export(rNmixture_s)
-export(rNmixture_v)
-export(rNmixture_BNB_oneObs)
-export(rNmixture_BNB_v)
-export(rNmixture_BNB_s)
-export(rNmixture_BBP_oneObs)
-export(rNmixture_BBP_v)
-export(rNmixture_BBP_s)
+export(rNmixtureAD_BBNB_oneObs)
+export(rNmixtureAD_BBNB_s)
+export(rNmixtureAD_BBNB_v)
+export(rNmixtureAD_BBP_oneObs)
+export(rNmixtureAD_BBP_s)
+export(rNmixtureAD_BBP_v)
+export(rNmixtureAD_BNB_oneObs)
+export(rNmixtureAD_BNB_s)
+export(rNmixtureAD_BNB_v)
+export(rNmixtureAD_s)
+export(rNmixtureAD_v)
 export(rNmixture_BBNB_oneObs)
-export(rNmixture_BBNB_v)
 export(rNmixture_BBNB_s)
-export(nimNmixPois_logFac)
+export(rNmixture_BBNB_v)
+export(rNmixture_BBP_oneObs)
+export(rNmixture_BBP_s)
+export(rNmixture_BBP_v)
+export(rNmixture_BNB_oneObs)
+export(rNmixture_BNB_s)
+export(rNmixture_BNB_v)
+export(rNmixture_s)
+export(rNmixture_v)
 export(rOcc_s)
 export(rOcc_v)
-export(nimBetaFun)
-export(dBetaBinom)
-export(dBetaBinom_One)
-export(rBetaBinom)
-export(rBetaBinom_One)
 import(nimble)
 importFrom(stats,dbinom)
+importFrom(stats,dnbinom)
+importFrom(stats,dpois)
+importFrom(stats,qnbinom)
+importFrom(stats,qpois)
+importFrom(stats,rbeta)
 importFrom(stats,rbinom)
+importFrom(stats,rnbinom)
+importFrom(stats,rpois)
 importFrom(stats,runif)
-importFrom("stats", "dpois", "qpois", "rpois", "dnbinom", "rnbinom", "rbeta", "qnbinom")