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:
nimbleEcology_0.5.0.tar.gz
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nimbleEcology.pdf |nimbleEcology.html✨
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
Last updated 1 months agofrom:3cbec00794. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win | OK | Nov 12 2024 |
| R-4.5-linux | OK | Nov 12 2024 |
| R-4.4-win | OK | Nov 12 2024 |
| R-4.4-mac | OK | Nov 12 2024 |
| R-4.3-win | OK | Nov 12 2024 |
| R-4.3-mac | OK | Nov 12 2024 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A beta binomial distribution and beta function for use in 'nimble' models | dBetaBinom dBetaBinom_s dBetaBinom_v nimBetaFun rBetaBinom_s rBetaBinom_v |
| Cormack-Jolly-Seber distribution for use in 'nimble' models | dCJS 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' models | dDHMM 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' models | dHMM dHMMo rHMM rHMMo |
| dNmixture distribution for use in 'nimble' models | dNmixture 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 distributions | dNmixture_BBNB_steps dNmixture_BBP_steps dNmixture_BNB_steps dNmixture_steps nimNmixPois_logFac |
| N-mixture distributions with AD support for use in 'nimble' models | dNmixtureAD 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' models | dOcc dOcc_s dOcc_v rOcc_s rOcc_v |