Package: nimbleEcology 0.5.0

Benjamin R. Goldstein

nimbleEcology: Distributions for Ecological Models in 'nimble'

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>).

Authors:Benjamin R. Goldstein [aut, cre], Daniel Turek [aut], Lauren Ponisio [aut], Wei Zhang [ctb], Perry de Valpine [aut]

nimbleEcology_0.5.0.tar.gz
nimbleEcology_0.5.0.zip(r-4.7)nimbleEcology_0.5.0.zip(r-4.6)nimbleEcology_0.5.0.zip(r-4.5)
nimbleEcology_0.5.0.tgz(r-4.6-any)nimbleEcology_0.5.0.tgz(r-4.5-any)
nimbleEcology_0.5.0.tar.gz(r-4.7-any)nimbleEcology_0.5.0.tar.gz(r-4.6-any)
nimbleEcology_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nimbleEcology/json (API)
NEWS

# Install 'nimbleEcology' in R:
install.packages('nimbleEcology', repos = c('https://nimble-dev.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nimble-dev/nimbleecology/issues

On CRAN:

Conda:

7.10 score 18 stars 1 packages 157 scripts 290 downloads 1 mentions 98 exports 16 dependencies

Last updated from:c9739e73e3. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK150
source / vignettesOK228
linux-release-x86_64OK166
macos-release-arm64OK205
macos-oldrel-arm64OK183
windows-develOK159
windows-releaseOK135
windows-oldrelOK98
wasm-releaseOK130

Exports:dBetaBinom_sdBetaBinom_vdCJS_ssdCJS_svdCJS_vsdCJS_vvdDHMMdDHMModDynOcc_ssmdDynOcc_sssdDynOcc_ssvdDynOcc_svmdDynOcc_svsdDynOcc_svvdDynOcc_vsmdDynOcc_vssdDynOcc_vsvdDynOcc_vvmdDynOcc_vvsdDynOcc_vvvdHMMdHMModNmixture_BBNB_oneObsdNmixture_BBNB_sdNmixture_BBNB_stepsdNmixture_BBNB_vdNmixture_BBP_oneObsdNmixture_BBP_sdNmixture_BBP_stepsdNmixture_BBP_vdNmixture_BNB_oneObsdNmixture_BNB_sdNmixture_BNB_stepsdNmixture_BNB_vdNmixture_sdNmixture_stepsdNmixture_vdNmixtureAD_BBNB_oneObsdNmixtureAD_BBNB_sdNmixtureAD_BBNB_vdNmixtureAD_BBP_oneObsdNmixtureAD_BBP_sdNmixtureAD_BBP_vdNmixtureAD_BNB_oneObsdNmixtureAD_BNB_sdNmixtureAD_BNB_vdNmixtureAD_sdNmixtureAD_vdOcc_sdOcc_vnimBetaFunnimNmixPois_logFacrBetaBinom_srBetaBinom_vrCJS_ssrCJS_svrCJS_vsrCJS_vvrDHMMrDHMMorDynOcc_ssmrDynOcc_sssrDynOcc_ssvrDynOcc_svmrDynOcc_svsrDynOcc_svvrDynOcc_vsmrDynOcc_vssrDynOcc_vsvrDynOcc_vvmrDynOcc_vvsrDynOcc_vvvrHMMrHMMorNmixture_BBNB_oneObsrNmixture_BBNB_srNmixture_BBNB_vrNmixture_BBP_oneObsrNmixture_BBP_srNmixture_BBP_vrNmixture_BNB_oneObsrNmixture_BNB_srNmixture_BNB_vrNmixture_srNmixture_vrNmixtureAD_BBNB_oneObsrNmixtureAD_BBNB_srNmixtureAD_BBNB_vrNmixtureAD_BBP_oneObsrNmixtureAD_BBP_srNmixtureAD_BBP_vrNmixtureAD_BNB_oneObsrNmixtureAD_BNB_srNmixtureAD_BNB_vrNmixtureAD_srNmixtureAD_vrOcc_srOcc_v

Dependencies:clicodacpp11glueigraphlatticelifecyclemagrittrMatrixnimblenumDerivpkgconfigpracmaR6rlangvctrs

Introduction to nimbleEcology

Perry de Valpine and Ben Goldstein

Rendered fromIntroduction_to_nimbleEcology.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2024-06-27
Started: 2019-09-10

Readme and manuals

Help Manual

Help pageTopics
A beta binomial distribution and beta function for use in 'nimble' modelsdBetaBinom dBetaBinom_s dBetaBinom_v nimBetaFun rBetaBinom_s rBetaBinom_v
Cormack-Jolly-Seber distribution for use in 'nimble' modelsdCJS dCJS_ss dCJS_sv dCJS_vs dCJS_vv rCJS_ss rCJS_sv rCJS_vs rCJS_vv
Dynamic Hidden Markov Model distribution for use in 'nimble' modelsdDHMM dDHMMo rDHMM rDHMMo
Dynamic occupancy distribution for use in 'nimble' models 'dDynOcc_**' and 'rDynOcc_**' provide dynamic occupancy model distributions that can be used directly from R or in 'nimble' models.dDynOcc dDynOcc_ssm dDynOcc_sss dDynOcc_ssv dDynOcc_svm dDynOcc_svs dDynOcc_svv dDynOcc_vsm dDynOcc_vss dDynOcc_vsv dDynOcc_vvm dDynOcc_vvs dDynOcc_vvv rDynOcc_ssm rDynOcc_sss rDynOcc_ssv rDynOcc_svm rDynOcc_svs rDynOcc_svv rDynOcc_vsm rDynOcc_vss rDynOcc_vsv rDynOcc_vvm rDynOcc_vvs rDynOcc_vvv
Hidden Markov Model distribution for use in 'nimble' modelsdHMM dHMMo rHMM rHMMo
dNmixture distribution for use in 'nimble' modelsdNmixture dNmixture_BBNB_oneObs dNmixture_BBNB_s dNmixture_BBNB_v dNmixture_BBP_oneObs dNmixture_BBP_s dNmixture_BBP_v dNmixture_BNB_oneObs dNmixture_BNB_s dNmixture_BNB_v dNmixture_s dNmixture_v rNmixture_BBNB_oneObs rNmixture_BBNB_s rNmixture_BBNB_v rNmixture_BBP_oneObs rNmixture_BBP_s rNmixture_BBP_v rNmixture_BNB_oneObs rNmixture_BNB_s rNmixture_BNB_v rNmixture_s rNmixture_v
Internal helper nimbleFunctions for dNmixture distributionsdNmixture_BBNB_steps dNmixture_BBP_steps dNmixture_BNB_steps dNmixture_steps nimNmixPois_logFac
N-mixture distributions with AD support for use in 'nimble' modelsdNmixtureAD dNmixtureAD_BBNB_oneObs dNmixtureAD_BBNB_s dNmixtureAD_BBNB_v dNmixtureAD_BBP_oneObs dNmixtureAD_BBP_s dNmixtureAD_BBP_v dNmixtureAD_BNB_oneObs dNmixtureAD_BNB_s dNmixtureAD_BNB_v dNmixtureAD_s dNmixtureAD_v rNmixtureAD_BBNB_oneObs rNmixtureAD_BBNB_s rNmixtureAD_BBNB_v rNmixtureAD_BBP_oneObs rNmixtureAD_BBP_s rNmixtureAD_BBP_v rNmixtureAD_BNB_oneObs rNmixtureAD_BNB_s rNmixtureAD_BNB_v rNmixtureAD_s rNmixtureAD_v
Occupancy distribution suitable for use in 'nimble' modelsdOcc dOcc_s dOcc_v rOcc_s rOcc_v