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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,35 @@ | ||
| Package: nimbleEcology | ||
| Type: Package | ||
| Title: Distributions for Ecological Models in 'nimble' | ||
| Version: 0.4.1 | ||
| Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu> | ||
| Version: 0.5.0 | ||
| Maintainer: Benjamin R. Goldstein <bgoldst2@ncsu.edu> | ||
| 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 | ||
| Copyright: Copyright (c) 2024, Perry de Valpine, Ben Goldstein, Daniel | ||
| Turek, Lauren Ponisio | ||
| Depends: R (>= 3.4.0), nimble | ||
| Depends: R (>= 4.0.0), nimble | ||
| Encoding: UTF-8 | ||
| VignetteBuilder: knitr | ||
| URL: https://github.com/nimble-dev/nimbleEcology | ||
| Collate: utils.R dBetaBinom.R dCJS.R dDynOcc.R dDHMM.R dHMM.R dOcc.R | ||
| dNmixture.R zzz.R | ||
| RoxygenNote: 7.1.2 | ||
| dNmixture.R dNmixtureAD.R zzz.R | ||
| RoxygenNote: 7.3.1 | ||
| Suggests: rmarkdown, knitr, testthat (>= 2.1.0) | ||
| NeedsCompilation: no | ||
| Packaged: 2021-11-01 17:11:05 UTC; ben | ||
| Packaged: 2024-06-27 00:06:32 UTC; dochv | ||
| Author: Benjamin R. Goldstein [aut, cre], | ||
| Daniel Turek [aut], | ||
| Lauren Ponisio [aut], | ||
| Wei Zhang [ctb], | ||
| Perry de Valpine [aut] | ||
| Repository: CRAN | ||
| Date/Publication: 2021-11-01 23:10:05 UTC | ||
| Date/Publication: 2024-06-27 10:00:02 UTC |
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|---|---|---|
| @@ -1,34 +1,40 @@ | ||
| 26c2a9885e932e80964c656bbfbccd33 *DESCRIPTION | ||
| d3cb955644283b138e3667d275547720 *NAMESPACE | ||
| 4568185c67fa0c1f7d7d489cd2825387 *R/dBetaBinom.R | ||
| d51730713ebb6ce2666e92d4617537e7 *R/dCJS.R | ||
| 048e10eb184c7c8a44fb314c95222dc5 *R/dDHMM.R | ||
| e64f3735cf3abedf8257acb7586db571 *R/dDynOcc.R | ||
| baed263cbc77d414a9c591c6c41b19d6 *R/dHMM.R | ||
| f8c7d976eb091332c340acd721cb7666 *R/dNmixture.R | ||
| 1773de33b066e63b57b05794b97aba0c *R/dOcc.R | ||
| 7b91316745a2054b3f9fe068756abbbb *R/utils.R | ||
| a9747bd996380c7268edf933bf827321 *R/zzz.R | ||
| 6060e4196696e7b43b635bd04ccbaf2f *README.md | ||
| 7836e1c8416e355f435e81b12daef0c8 *build/vignette.rds | ||
| d673da553bcaf0dc9669d53a91c412de *inst/CITATION | ||
| 1c2c09685c3e008a161cdb0dbcaac1c8 *inst/NEWS | ||
| e7d09570bcfa6d351777096ca6179ff4 *inst/doc/Introduction_to_nimbleEcology.R | ||
| 312b5bf7dab4e5cdcfa62e4070347985 *inst/doc/Introduction_to_nimbleEcology.Rmd | ||
| 44efa61267ba0d797e2f3b9b204794c2 *inst/doc/Introduction_to_nimbleEcology.html | ||
| 587e7dc0f10eab6efc8369cb86881a74 *man/dBetaBinom.Rd | ||
| d1db4fb63522a576d67a1dda1ac6995d *man/dCJS.Rd | ||
| 96ef7b9552b112c81404048e25ab53c8 *man/dDHMM.Rd | ||
| 9eb084ac4e3ffef4a974d21aecab3993 *man/dDynOcc.Rd | ||
| 59e32092163753298e1574753e9e0187 *man/dHMM.Rd | ||
| 3132f8944f8832d268c4c2ca56007e84 *man/dNmixture.Rd | ||
| 610a4c66249fc74a1877e6ac0bb2c934 *man/dOcc.Rd | ||
| 87d0a8d9c1eaaa4d9155bff39c4a3f5e *man/nimNmixPois_logFac.Rd | ||
| c84c6e2b17798d1e2a6c963432993003 *tests/testthat/test-BetaBinom.R | ||
| 46659474392b5e97dfc91fd984da6165 *tests/testthat/test-CJS.R | ||
| ea79f4e017c7eaf2d6f68b4e5295823a *tests/testthat/test-DHMM.R | ||
| 64f741bfc86087ab7ae351af22cfbb33 *tests/testthat/test-DynOcc.R | ||
| 2f8639be4da363d2385aba7bd87f693e *tests/testthat/test-HMM.R | ||
| 15325aa96e2f5ea1154b825f1a00916d *tests/testthat/test-Nmixture.R | ||
| ad4a97f8d4a6789b26ca9e904c84c4f3 *tests/testthat/test-Occ.R | ||
| 312b5bf7dab4e5cdcfa62e4070347985 *vignettes/Introduction_to_nimbleEcology.Rmd | ||
| d32551b8a447d3e4ea33eb69abe34aae *DESCRIPTION | ||
| a993cfffce3ab489d6d688c0866f0061 *NAMESPACE | ||
| b30c31e401c36e8c3bafb75dc9f3526c *R/dBetaBinom.R | ||
| 3d69897863b1582038ed30f0bce68e63 *R/dCJS.R | ||
| 1626ac08a2ee15bb8e78ef2759661a32 *R/dDHMM.R | ||
| ea645779436a1cc0c00b6057506b69c4 *R/dDynOcc.R | ||
| c5467b15e7a9040de3b7dd0da513a74f *R/dHMM.R | ||
| 46c796d2903b8867cd9dcd5bed5db133 *R/dNmixture.R | ||
| 03b244df09a27f6161231dd34b179bef *R/dNmixtureAD.R | ||
| 98d34d88cbc5152dd8a3c73b7be98262 *R/dOcc.R | ||
| f9d1eced0a06f2dfcd2aeb129b61542c *R/utils.R | ||
| c7a685269bdc6cfbbf10079aee6ec99e *R/zzz.R | ||
| 58f1a4deacda8a135ba04482c261813d *README.md | ||
| 92221f4785547c7015c49bf726a4844d *build/vignette.rds | ||
| 6b428c25196bb1bcf238216e52e400cb *inst/AD_test_utils.R | ||
| fdc515e22190c8b8e7ee7b92de714dd7 *inst/CITATION | ||
| bd3736b748e5af1fc64b9614e9b35089 *inst/NEWS | ||
| 39c8af915adb0f0db44b112f5f65d5f1 *inst/doc/Introduction_to_nimbleEcology.R | ||
| c99db65b172372db1303c97c2ee93164 *inst/doc/Introduction_to_nimbleEcology.Rmd | ||
| 887722acef9b12b17d1e13265de38e14 *inst/doc/Introduction_to_nimbleEcology.html | ||
| dc0ced207f97e32b3f9d244b967f0f8f *inst/test_utils.R | ||
| 9fe3ad201034ebe5fd5b377701db3d64 *man/dBetaBinom.Rd | ||
| 1879248d65242994a91788c65fa37b1a *man/dCJS.Rd | ||
| a7e590507b34a8605b3fa4a91a029983 *man/dDHMM.Rd | ||
| 9a301c9081b825a4eb3a59b494dc9f31 *man/dDynOcc.Rd | ||
| 9ed3b0860fbb916344cd3b013d838dd1 *man/dHMM.Rd | ||
| 341871a390333d0bc71aca65671e75bf *man/dNmixture.Rd | ||
| 8806ef5cbe6cda606534a32178636e4b *man/dNmixtureAD.Rd | ||
| 5329d074c0ea63c12a6fa8410290b0da *man/dNmixture_steps.Rd | ||
| ebb8e9fba309b2f652cc6c0714bd4235 *man/dOcc.Rd | ||
| afff4c47e4b23b3b09680f4c76170221 *tests/testthat/test-AD.R | ||
| 08e63fee47a7f97c1c4ac241ff8713fe *tests/testthat/test-BetaBinom.R | ||
| 6ebb620483cde0ee02195969601f164d *tests/testthat/test-CJS.R | ||
| 3bcc2eb40b01ba632a43fbe057db6ada *tests/testthat/test-DHMM.R | ||
| e358fdb0a96f02a5c239eed296b75161 *tests/testthat/test-DynOcc.R | ||
| 999c063b80d6d2c48db424b579657b9d *tests/testthat/test-HMM.R | ||
| b3c4f1c3198951da81d330150d01587c *tests/testthat/test-Nmixture.R | ||
| b58a9b1631c014066619d10a51fdfdae *tests/testthat/test-NmixtureADnoDerivs.R | ||
| fbcb9f3e25072ab02c581c4bdd95e098 *tests/testthat/test-Occ.R | ||
| c99db65b172372db1303c97c2ee93164 *vignettes/Introduction_to_nimbleEcology.Rmd |
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|
|
||
| export(dCJS_ss) | ||
| export(dCJS_sv) | ||
| export(dCJS_vs) | ||
| export(dCJS_vv) | ||
| export(dDHMM) | ||
| export(dDHMMo) | ||
| export(dDynOcc_ssm) | ||
| export(dDynOcc_sss) | ||
| export(dDynOcc_ssv) | ||
| export(dDynOcc_svm) | ||
| export(dDynOcc_svs) | ||
| export(dDynOcc_svv) | ||
| export(dDynOcc_vsm) | ||
| export(dDynOcc_vss) | ||
| export(dDynOcc_vsv) | ||
| export(dDynOcc_vvm) | ||
| 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(dNmixture_BBNB_oneObs) | ||
| export(dNmixture_BBNB_v) | ||
| export(dNmixture_BBNB_s) | ||
| export(dOcc_s) | ||
| export(dOcc_v) | ||
| export(rCJS_ss) | ||
| export(rCJS_sv) | ||
| export(rCJS_vs) | ||
| export(rCJS_vv) | ||
| export(rDHMM) | ||
| export(rDHMMo) | ||
| export(rDynOcc_ssm) | ||
| export(rDynOcc_sss) | ||
| export(rDynOcc_ssv) | ||
| export(rDynOcc_svm) | ||
| export(rDynOcc_svs) | ||
| export(rDynOcc_svv) | ||
| export(rDynOcc_vsm) | ||
| export(rDynOcc_vss) | ||
| export(rDynOcc_vsv) | ||
| export(rDynOcc_vvm) | ||
| 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(rNmixture_BBNB_oneObs) | ||
| export(rNmixture_BBNB_v) | ||
| export(rNmixture_BBNB_s) | ||
| export(nimNmixPois_logFac) | ||
| 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,rbinom) | ||
| importFrom(stats,runif) | ||
| importFrom("stats", "dpois", "qpois", "rpois", "dnbinom", "rnbinom", "rbeta", "qnbinom") | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| export(dBetaBinom_s) | ||
| export(dBetaBinom_v) | ||
| export(dCJS_ss) | ||
| export(dCJS_sv) | ||
| export(dCJS_vs) | ||
| export(dCJS_vv) | ||
| export(dDHMM) | ||
| export(dDHMMo) | ||
| export(dDynOcc_ssm) | ||
| export(dDynOcc_sss) | ||
| export(dDynOcc_ssv) | ||
| export(dDynOcc_svm) | ||
| export(dDynOcc_svs) | ||
| export(dDynOcc_svv) | ||
| export(dDynOcc_vsm) | ||
| export(dDynOcc_vss) | ||
| export(dDynOcc_vsv) | ||
| export(dDynOcc_vvm) | ||
| export(dDynOcc_vvs) | ||
| export(dDynOcc_vvv) | ||
| export(dHMM) | ||
| export(dHMMo) | ||
| 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_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) | ||
| export(rCJS_vv) | ||
| export(rDHMM) | ||
| export(rDHMMo) | ||
| export(rDynOcc_ssm) | ||
| export(rDynOcc_sss) | ||
| export(rDynOcc_ssv) | ||
| export(rDynOcc_svm) | ||
| export(rDynOcc_svs) | ||
| export(rDynOcc_svv) | ||
| export(rDynOcc_vsm) | ||
| export(rDynOcc_vss) | ||
| export(rDynOcc_vsv) | ||
| export(rDynOcc_vvm) | ||
| export(rDynOcc_vvs) | ||
| export(rDynOcc_vvv) | ||
| export(rHMM) | ||
| export(rHMMo) | ||
| 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_s) | ||
| 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) | ||
| 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) |
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