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| Package: Petersen | ||
| Type: Package | ||
| Title: Estimators for Two-Sample Capture-Recapture Studies | ||
| Version: 2023.12.1 | ||
| Date: 2023-12-01 | ||
| Authors@R: person("Carl", "Schwarz", email = "cschwarz.stat.sfu.ca@gmail.com", role = c("aut", "cre")) | ||
| Description: A comprehensive implementation of Petersen-type estimators | ||
| and its many variants for two-sample capture-recapture studies. | ||
| A conditional likelihood approach is used that allows | ||
| for tag loss; non reporting of tags; reward tags; categorical, geographical and temporal stratification; | ||
| partial stratification; reverse capture-recapture; | ||
| and continuous variables in modeling the probability of capture. | ||
| Many examples from fisheries management are presented. | ||
| License: GPL-2 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.2.3 | ||
| Imports: AICcmodavg, bbmle, BTSPAS, formula.tools, ggplot2, MASS, | ||
| Matrix, msm, numDeriv, plyr, reshape2, rlang, SPAS, stats, | ||
| stringr, tidyr, utils | ||
| Depends: R (>= 2.10) | ||
| Suggests: knitr, rmarkdown, R.rsp | ||
| VignetteBuilder: knitr, rmarkdown, R.rsp | ||
| URL: https://github.com/cschwarz-stat-sfu-ca/Petersen | ||
| BugReports: https://github.com/cschwarz-stat-sfu-ca/Petersen/issues | ||
| NeedsCompilation: no | ||
| Packaged: 2023-11-11 20:32:28 UTC; cschwarz | ||
| Author: Carl Schwarz [aut, cre] | ||
| Maintainer: Carl Schwarz <cschwarz.stat.sfu.ca@gmail.com> | ||
| Repository: CRAN | ||
| Date/Publication: 2023-11-12 12:03:24 UTC |
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| 7d3427d558ac8821bf54b10d08b87ed3 *DESCRIPTION | ||
| 2a5cccf1a93d61dcdf849c3c327dd13f *NAMESPACE | ||
| aa13c3ff2f22042582820a439c17e9e7 *NEWS.md | ||
| 0afa7fd62c2fa69061a1517c98346380 *R/IS.code.R | ||
| 5474d929b0fed294fd7fbd71e5a9bcfd *R/LP_AICc.R | ||
| f656c9d1cd5403b7935791379271b9f9 *R/LP_BTSPAS_est.R | ||
| cec7035f5a7b43592e0101cd24320589 *R/LP_BTSPAS_fit_Diag.R | ||
| 5cbe35f4442f90b93fba0b9ed3a7067f *R/LP_BTSPAS_fit_NonDiag.R | ||
| 68ecfd0e439612c093732ca3ed17b091 *R/LP_CL_fit.r | ||
| 6d652a14f4d0c73e9939a78c978feebb *R/LP_IS_est.R | ||
| c65ee6cf6c12719c3a4b763e8a46e0a1 *R/LP_IS_fit.R | ||
| 183aa179d50c264e8504ea5533008e26 *R/LP_IS_print.R | ||
| af40324152b6c6a2994df947a163ef96 *R/LP_SPAS_est.R | ||
| 3fadfbaae51caa865e879dde8366de2f *R/LP_SPAS_fit.R | ||
| 2e5c7d7bcaf71de3fbec69879e4f226c *R/LP_TL_cond_lik.R | ||
| 46f5f2d2245f53b7fa83005ad5e71738 *R/LP_TL_est.R | ||
| ac9f15578e8004935fa3d0aab6da8465 *R/LP_TL_fit.R | ||
| 93a67fcfdae67e804f38dfe5f9798e76 *R/LP_TL_simulate.R | ||
| c3dfeece60b213f379ee8ce852f85467 *R/LP_cond_lik.R | ||
| fbdb773fab30da7d48b743de604ceb0b *R/LP_est.R | ||
| d89f5584196dd4c6a2dd06cb8341feef *R/LP_est_adjust.R | ||
| 7fa84ccab29b104f4fc5e1b51025b729 *R/LP_fit.R | ||
| 94ee9e4bf48580e25e0481f0a93b5bcf *R/LP_modavg.R | ||
| d1cc6265787da5207b682dbca1be10ca *R/LP_summary_stats.R | ||
| 938039511c6df220a3559d828d9efd65 *R/LP_test_equal_mf.R | ||
| fe862e6b6a361632ab9a5fa2361b4f22 *R/LP_test_equal_recap.R | ||
| fb04aa69e6c888d1eb1c01aa21f48f79 *R/cap_hist_to_n_m_u.R | ||
| 57e3ba3c277038d87a48befa9b1eef60 *R/convert.estimate.se.to.alpha.beta.R | ||
| 4dda6629b5c6caccbdc922cd4c63f8c5 *R/data.R | ||
| 59890fdd37b815f343e12ac6b29cf989 *R/fit_classes.R | ||
| 4020fadf51fd1d666ad7f9a38cb7f464 *R/logit.R | ||
| 2dd4d4fe347094cd3fecb4012035f55d *R/split_cap_hist.R | ||
| 67d201e9c9040295e131e5c36972a79c *R/util.R | ||
| 4f4d002044593f7f15e1b0577986f5f4 *README.md | ||
| 8faf250d78a120ba4c7ea2186efddd24 *build/partial.rdb | ||
| acf30a5e5a3341098158d9fb11d08bb9 *build/vignette.rds | ||
| ac09c98f38ed74a0eef5e7e4d0c734bb *data/data_NorthernPike.rda | ||
| 0de07505f909190f8153544ba2700c4f *data/data_NorthernPike_tagloss.rda | ||
| 855d7e1a1e830df474ad79aef31fa3a6 *data/data_btspas_diag1.rda | ||
| 423a562c23e476d8c1023cd9872ce3e4 *data/data_btspas_nondiag1.rda | ||
| b1b968e350def5e1f646bd75e9ebe8a0 *data/data_kokanee_tagloss.rda | ||
| 20ac1c04f5f496dbbb1a04249d9ab65d *data/data_rodli.rda | ||
| 002000a739fb05c24140fe7cf813520a *data/data_sim_reward.rda | ||
| 53a1c497a87ba3e0fa762dd9da6c67e4 *data/data_sim_tagloss_t2perm.rda | ||
| 566384f6962fb06c4591c321700f65f0 *data/data_sim_tagloss_twoD.rda | ||
| 03cbe665dcf4aa362413e3f54c82dd54 *data/data_spas_harrison.rda | ||
| e4d5169d48e7c0bef024e18caf26bad1 *data/data_wae_is_long.rda | ||
| f33bd6ec6703acd9a2874d43984067a3 *data/data_wae_is_short.rda | ||
| 469774a3611bf4bdbb267a315b8ef951 *data/data_yukon_reverse.rda | ||
| d5a4a0703a177dbb99c2de902fb33ce1 *inst/CITATION | ||
| 46750e778a5cdb4d65c347f8e43df623 *inst/doc/PackageDocumentation.R | ||
| 7385ae8c839f4128a0452fea6d977723 *inst/doc/PackageDocumentation.Rmd | ||
| d0158384c88d81939092f778d7b5d3b5 *inst/doc/PackageDocumentation.html | ||
| 4e09906feebe50d449c333ed945ec24f *inst/extdata/PetersenWorkBook-2023-05-01.xls | ||
| a23e18190582f8ed578ff971ab7ab397 *man/LP_AICc.Rd | ||
| c218a3e669da0286366cfce4d53011b4 *man/LP_BTSPAS_est.Rd | ||
| 074882b14ddef7354f2594de93790fb5 *man/LP_BTSPAS_fit_Diag.Rd | ||
| 0017c100cf500cefa7a37a6ba96e9bb1 *man/LP_BTSPAS_fit_NonDiag.Rd | ||
| 52347a2f908e08ae822f857a9b6814ec *man/LP_CL_fit.Rd | ||
| b679f114c276f2a6d2db2bdf4d534e84 *man/LP_IS_est.Rd | ||
| 2f310fc82c9891c834f171aec83bb461 *man/LP_IS_fit.Rd | ||
| fd0a62a601ae9ba191c36bffc2f689a8 *man/LP_IS_print.Rd | ||
| 259c8f2712724787d942da75d24283d4 *man/LP_SPAS_est.Rd | ||
| c08e079ce32e226fbbfbed874a3caa8a *man/LP_SPAS_fit.Rd | ||
| e82043dfaa1cfb05e75bfd6adcf0074a *man/LP_TL_est.Rd | ||
| df6be01f6291a58b92723dcef8289225 *man/LP_TL_fit.Rd | ||
| 6388afe15359e70b1194fa45a00e1f3c *man/LP_TL_simulate.Rd | ||
| 0d00d3530b78fe31cc433879999e8ed8 *man/LP_est.Rd | ||
| 50c0b227985230d7d57721c9d9fcc546 *man/LP_est_adjust.Rd | ||
| 51296d0ac1150027f47fae6a378c6a7e *man/LP_fit.Rd | ||
| 8b68896311bbf6295a4554c305c7a84a *man/LP_modavg.Rd | ||
| 7d07993fce536d2fc12f8dda4f6adc83 *man/LP_summary_stats.Rd | ||
| e94cd2d8a15d2316cf98eaf7e3a165f7 *man/LP_test_equal_mf.Rd | ||
| a15f13a13c60b8887d3fe6a3446ba21b *man/LP_test_equal_recap.Rd | ||
| 3f3f7708a325f857bf08ff28db770c1c *man/cap_hist_to_n_m_u.Rd | ||
| 6db0c8c86517a9b6aa60605a691a41fc *man/data_NorthernPike.Rd | ||
| eff8771b7e1eecf1322d8a2d4be2c0bb *man/data_NorthernPike_tagloss.Rd | ||
| 8133581fe068d762ccad1946f89f07a8 *man/data_btspas_diag1.Rd | ||
| 68ed6b0d40afd787c47989f78cc64149 *man/data_btspas_nondiag1.Rd | ||
| c511dee60fc63266bc8e1d742740df8c *man/data_kokanee_tagloss.Rd | ||
| 2b49dc3106d8da0d33f07fe82cc99a58 *man/data_rodli.Rd | ||
| eb3236ca93e330ffc9c10015697a9f26 *man/data_sim_reward.Rd | ||
| 88c0b497e817631fe8bb4af3368f2bd1 *man/data_sim_tagloss_t2perm.Rd | ||
| 8274f9a35e35564c628b6925556d6fad *man/data_sim_tagloss_twoD.Rd | ||
| dc8941475788d18311700d4805ce696f *man/data_spas_harrison.Rd | ||
| 2b03b5fdd3d2fb24d7e570d33c3e6ad8 *man/data_wae_is_long.Rd | ||
| b1c75dc5ea997282be6cbe3bbe403051 *man/data_wae_is_short.Rd | ||
| 81a454cdda18e93d2a9cc07a9f741e8d *man/data_yukon_reverse.Rd | ||
| ce7961f293e7351cacbe72ba79dd15d2 *man/fit_classes.Rd | ||
| c04571584e77645bfa53a27b625381ec *man/logit.Rd | ||
| 7ece952b57ff54f35203f7f56cc86400 *man/split_cap_hist.Rd | ||
| 7385ae8c839f4128a0452fea6d977723 *vignettes/PackageDocumentation.Rmd |
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| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| export(LP_AICc) | ||
| export(LP_BTSPAS_est) | ||
| export(LP_BTSPAS_fit_Diag) | ||
| export(LP_BTSPAS_fit_NonDiag) | ||
| export(LP_CL_fit) | ||
| export(LP_IS_est) | ||
| export(LP_IS_fit) | ||
| export(LP_IS_print) | ||
| export(LP_SPAS_est) | ||
| export(LP_SPAS_fit) | ||
| export(LP_TL_est) | ||
| export(LP_TL_fit) | ||
| export(LP_TL_simulate) | ||
| export(LP_est) | ||
| export(LP_est_adjust) | ||
| export(LP_fit) | ||
| export(LP_modavg) | ||
| export(LP_summary_stats) | ||
| export(LP_test_equal_mf) | ||
| export(LP_test_equal_recap) | ||
| export(cap_hist_to_n_m_u) | ||
| export(expit) | ||
| export(fit_classes) | ||
| export(logit) | ||
| export(split_cap_hist) | ||
| import(ggplot2) | ||
| importFrom(AICcmodavg,AICcCustom) | ||
| importFrom(AICcmodavg,modavgCustom) | ||
| importFrom(BTSPAS,TimeStratPetersenDiagError_fit) | ||
| importFrom(BTSPAS,TimeStratPetersenNonDiagErrorNP_fit) | ||
| importFrom(MASS,ginv) | ||
| importFrom(Matrix,bdiag) | ||
| importFrom(SPAS,SPAS.fit.model) | ||
| importFrom(bbmle,mle2) | ||
| importFrom(formula.tools,is.one.sided) | ||
| importFrom(graphics,hist) | ||
| importFrom(msm,deltamethod) | ||
| importFrom(numDeriv,hessian) | ||
| importFrom(plyr,ddply) | ||
| importFrom(plyr,is.formula) | ||
| importFrom(plyr,l_ply) | ||
| importFrom(plyr,ldply) | ||
| importFrom(plyr,llply) | ||
| importFrom(reshape2,melt) | ||
| importFrom(rlang,.data) | ||
| importFrom(stats,as.formula) | ||
| importFrom(stats,coef) | ||
| importFrom(stats,dnorm) | ||
| importFrom(stats,model.matrix) | ||
| importFrom(stats,na.pass) | ||
| importFrom(stats,optim) | ||
| importFrom(stats,qnorm) | ||
| importFrom(stats,quantile) | ||
| importFrom(stats,rbeta) | ||
| importFrom(stats,rnorm) | ||
| importFrom(stats,runif) | ||
| importFrom(stats,sd) | ||
| importFrom(stats,var) | ||
| importFrom(stats,xtabs) | ||
| importFrom(stringr,fixed) | ||
| importFrom(stringr,str_split_fixed) | ||
| importFrom(tidyr,pivot_wider) | ||
| importFrom(utils,head) | ||
| importFrom(utils,tail) |
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|
|
||
| Petersen 2023.12.01 | ||
| --------------- | ||
|
|
||
| * Initial release. |
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