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AD support #27

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merged 43 commits into from
Jun 25, 2024
Merged

AD support #27

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5adf10c
enableDerivs flags for AD
dochvam Jun 8, 2020
bcc8940
change variables to integers for AD
dochvam Jun 12, 2020
e637a70
Update dDynOcc_sss and dHMM to use new AD features to work.
perrydv Jun 17, 2020
ffcc5fc
Merge branch 'AD_0.3' of https://github.com/nimble-dev/nimbleEcology …
perrydv Jun 17, 2020
a195c99
update dDynOcc to allow AD; build Travis from ADoak
dochvam Jun 17, 2020
342fc4f
update *HMM* to allow AD
dochvam Jun 17, 2020
1c922a5
adding AD changes to HMM, DHMM
dochvam Jun 17, 2020
20593df
draft updates to dHMMo
perrydv Jun 17, 2020
fa3283b
DHMM and HMM AD fix line
dochvam Jun 17, 2020
71f4f8e
Add AD tests for each dist function (other than Nmix)
dochvam Jun 19, 2020
b43ed6a
see if I can get Travis to use ADoak for package building
dochvam Jun 19, 2020
3cfc98e
update buildDerivs syntax
perrydv May 23, 2022
5edae30
merge changes from main branch
Jun 3, 2022
d308b34
add up-to-date AD testing file
Jun 3, 2022
194380b
work on implementing AD tests
dochvam Jun 3, 2022
a0d13fe
implement AD tests for at least one of each dist
dochvam Jun 7, 2022
89170c7
build out AD test suite
dochvam Jun 13, 2022
742248a
see if test-AD will run on Github
dochvam Jun 22, 2022
b062e6b
ask Github to install NIMBLE from AD branch
dochvam Jun 22, 2022
1a5f4c8
add test_utils to nE inst
dochvam Jun 22, 2022
bba7385
use test_that in test-AD; add numDerivs to depends
dochvam Jun 22, 2022
4ef93fd
ask for tests on AD-rc0 branch
dochvam Jun 22, 2022
dcd7eee
remove pipe from AD_test_utils
dochvam Jun 22, 2022
58a0a2a
add pracma to depends
dochvam Jun 22, 2022
70b2be6
adjust dhmm tol
dochvam Jun 23, 2022
6a177e3
tweak ad tols further
dochvam Jun 23, 2022
699db08
check all tols
dochvam Jun 23, 2022
6bee0fd
install nimble from AD branch on Windows
dochvam Jun 23, 2022
a738004
use remotes instead of devtools
dochvam Jun 23, 2022
4febeac
try putting pracma and numDerivs as installs for testing, not depends
dochvam Jun 23, 2022
3b313e3
check that N-mixture errors
dochvam Jun 23, 2022
41c985e
AD support. roxygen. refactored dNmixture.
perrydv Jun 22, 2024
0dba4d0
update YAML so tests run
dochvam Jun 22, 2024
e7217e4
switch to supported version of ubuntu for github action
dochvam Jun 22, 2024
f8efafc
updates to BetaBinom, yaml, tests, documentation
perrydv Jun 23, 2024
31cef5d
update check.yaml
perrydv Jun 23, 2024
e58ce4e
fix dNmixture_BBP_s
perrydv Jun 23, 2024
ec6be9e
tweak dDHMM AD test tolderance
perrydv Jun 23, 2024
4f134ed
more fixed tests
perrydv Jun 23, 2024
1b7fe74
Update check_windows.yaml
perrydv Jun 24, 2024
21d9bab
try fiddling with yaml Linux content
perrydv Jun 24, 2024
04fa46b
Update DESCRIPTION
perrydv Jun 24, 2024
6ed4f42
edits to Nmix description, pkg description
dochvam Jun 24, 2024
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22 changes: 15 additions & 7 deletions .github/workflows/check.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,12 @@ on:
branches:
- main
- master
- AD-rc0
pull_request:
branches:
- main
- master
- AD-rc0

name: R-CMD-check

Expand All @@ -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
Expand All @@ -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: |
Expand All @@ -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
Expand Down
10 changes: 8 additions & 2 deletions .github/workflows/check_windows.yaml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,12 @@ on:
branches:
- main
- master
- AD-rc0
pull_request:
branches:
- main
- master
- AD-rc0

name: R-CMD-check

Expand All @@ -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: |
Expand Down Expand Up @@ -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
Expand Down
14 changes: 8 additions & 6 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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,
Expand Down
83 changes: 58 additions & 25 deletions NAMESPACE
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Original file line number Diff line number Diff line change
@@ -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)
Expand All @@ -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)
Expand All @@ -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")
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