Philosophy | Installation | Getting Help | Providing Data | Recruitment | Fit a Bayesian model | Convergence | Summary | Priors | Survival | Predictions | Recruitment by year | Recruitment for a 'typical' year | Recruitment trend | Survival by year for a 'typical' month | Survival by month for a 'typical' year | Population Growth | Multi-Population Analysis | Maximum Likelihood | Understanding bboufit objects | References
Package: bboutools 1.3.0.9003
Seb Dalgarno
bboutools: Boreal Caribou Survival, Recruitment and Population Growth
Estimates annual survival, recruitment and population growth for boreal caribou populations using Bayesian and Maximum Likelihood models with fixed and random effects.
Authors:
bboutools_1.3.0.9003.tar.gz
bboutools_1.3.0.9003.zip(r-4.7)bboutools_1.3.0.9003.zip(r-4.6)bboutools_1.3.0.9003.zip(r-4.5)
bboutools_1.3.0.9003.tgz(r-4.6-any)bboutools_1.3.0.9003.tgz(r-4.5-any)
bboutools_1.3.0.9003.tar.gz(r-4.7-any)bboutools_1.3.0.9003.tar.gz(r-4.6-any)
bboutools_1.3.0.9003.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bboutools/json (API)
| # Install 'bboutools' in R: |
| install.packages('bboutools', repos = c('https://poissonconsulting.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/poissonconsulting/bboutools/issues
Pkgdown/docs site:https://poissonconsulting.github.io
Last updated from:09499ac5b6. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 933 | ||
| source / vignettes | OK | 236 | ||
| linux-release-x86_64 | OK | 923 | ||
| macos-release-arm64 | OK | 565 | ||
| macos-oldrel-arm64 | OK | 854 | ||
| windows-devel | OK | 873 | ||
| windows-release | OK | 915 | ||
| windows-oldrel | OK | 783 | ||
| wasm-release | OK | 144 |
Exports:augmentbb_fit_recruitmentbb_fit_recruitment_mlbb_fit_survivalbb_fit_survival_mlbb_plot_monthbb_plot_month_survivalbb_plot_yearbb_plot_year_calf_cow_ratiobb_plot_year_growthbb_plot_year_population_changebb_plot_year_recruitmentbb_plot_year_survivalbb_plot_year_trend_calf_cow_ratiobb_plot_year_trend_recruitmentbb_plot_year_trend_survivalbb_predict_calf_cow_ratiobb_predict_calf_cow_ratio_samplesbb_predict_calf_cow_ratio_trendbb_predict_calf_cow_ratio_trend_samplesbb_predict_growthbb_predict_growth_samplesbb_predict_lambdabb_predict_population_changebb_predict_population_change_samplesbb_predict_recruitmentbb_predict_recruitment_samplesbb_predict_recruitment_trendbb_predict_recruitment_trend_samplesbb_predict_survivalbb_predict_survival_samplesbb_predict_survival_trendbb_predict_survival_trend_samplesbb_priors_recruitmentbb_priors_recruitment_nationalbb_priors_survivalbb_priors_survival_nationalcoefconvergedesrestimatesglancelicensing_mdlogLikmodel_codemodel_recruitmentmodel_survivalnchainsnitersnobsnparsntermsparspredictrhatsamplestidy
Dependencies:abindbboudatabbouNationalPriorschkclicodacpp11dplyrextrasfarvergenericsggplot2gluegtablehmsigraphisobandlabelinglatticelifecyclemagrittrMatrixmcmcderivemcmcrnewdatanimblenimbleQuadnlistnumDerivpillarpkgconfigpolynompracmapurrrR6RColorBrewerrescalerlangS7scalesstringistringrtermtibbletidyrtidyselectuniversalsutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get Augmented Data from bboufit Object | augment.bboufit |
| Get Augmented Data from bboufit_ml Object | augment.bboufit_ml |
| Fit Recruitment Model | bb_fit_recruitment |
| Fit Recruitment Model with Maximum Likelihood | bb_fit_recruitment_ml |
| Fit Survival Model | bb_fit_survival |
| Fit Survival Model with Maximum Likelihood | bb_fit_survival_ml |
| Plot Month | bb_plot_month bb_plot_month.bboufit_survival bb_plot_month.data.frame |
| Plot Monthly Survival | bb_plot_month_survival bb_plot_month_survival.bboufit_survival bb_plot_month_survival.data.frame |
| Plot Year | bb_plot_year bb_plot_year.bboufit bb_plot_year.bboufit_ml bb_plot_year.data.frame |
| Plot Year Calf-Cow Ratio | bb_plot_year_calf_cow_ratio bb_plot_year_calf_cow_ratio.bboufit_recruitment bb_plot_year_calf_cow_ratio.data.frame |
| Plot Year Population Growth | bb_plot_year_growth |
| Plot Year Population Change | bb_plot_year_population_change |
| Plot Year Recruitment | bb_plot_year_recruitment bb_plot_year_recruitment.bboufit_recruitment bb_plot_year_recruitment.data.frame |
| Plot Year Survival | bb_plot_year_survival bb_plot_year_survival.bboufit_survival bb_plot_year_survival.data.frame |
| Plot Annual Calf-Cow Ratio Trend | bb_plot_year_trend_calf_cow_ratio bb_plot_year_trend_calf_cow_ratio.bboufit_recruitment bb_plot_year_trend_calf_cow_ratio.data.frame |
| Plot Annual Recruitment Trend | bb_plot_year_trend_recruitment bb_plot_year_trend_recruitment.bboufit_recruitment bb_plot_year_trend_recruitment.data.frame |
| Plot Annual Survival Trend | bb_plot_year_trend_survival bb_plot_year_trend_survival.bboufit_survival bb_plot_year_trend_survival.data.frame |
| Predict Calf-Cow Ratio | bb_predict_calf_cow_ratio |
| Predict Calf-Cow Ratio Samples | bb_predict_calf_cow_ratio_samples |
| Predict Calf-Cow Ratio Trend | bb_predict_calf_cow_ratio_trend |
| Predict Calf-Cow Ratio Trend Samples | bb_predict_calf_cow_ratio_trend_samples |
| Predict Population Growth Lambda | bb_predict_growth bb_predict_lambda |
| Predict Population Growth Lambda Samples | bb_predict_growth_samples |
| Predict Population Change | bb_predict_population_change |
| Predict Population Change Samples | bb_predict_population_change_samples |
| Predict Recruitment | bb_predict_recruitment |
| Predict Recruitment Samples | bb_predict_recruitment_samples |
| Predict Recruitment Trend | bb_predict_recruitment_trend |
| Predict Recruitment Trend Samples | bb_predict_recruitment_trend_samples |
| Predict Survival | bb_predict_survival |
| Predict Survival Samples | bb_predict_survival_samples |
| Predict Survival Trend | bb_predict_survival_trend |
| Predict Survival Trend Samples | bb_predict_survival_trend_samples |
| Recruitment model default priors | bb_priors_recruitment |
| Disturbance-informed national recruitment priors | bb_priors_recruitment_national |
| Survival model default priors | bb_priors_survival |
| Disturbance-informed national survival priors | bb_priors_survival_national |
| Get Tidy Tibble from bboufit Object. | coef.bboufit |
| Get Tidy Tibble from bboufit_ml Object. | coef.bboufit_ml |
| Get Convergence of bboufit Object | converged.bboufit |
| Get Convergence of bboufit_ml Object | converged.bboufit_ml |
| Get Effective Sample Rate of bboufit Object | esr.bboufit |
| Estimates for bboufit Object | estimates.bboufit |
| Estimates for bboufit_ml Object | estimates.bboufit_ml |
| Get a Glance Summary of bboufit Object | glance.bboufit |
| Get a Glance Summary of bboufit_ml Object | glance.bboufit_ml |
| Get Model Code | model_code model_code.bboufit model_code.bboufit_ml |
| Build Nimble recruitment model. | model_recruitment |
| Build Nimble survival model. | model_survival |
| Get Number of Chains from bboufit Object | nchains.bboufit |
| Get Number of Iterations from bboufit Object | niters.bboufit |
| Get Number of Parameters from bboufit Object | npars.bboufit |
| Get Number of Parameters from bboufit_ml Object | npars.bboufit_ml |
| Get Number of Terms from bboufit Object | nterms.bboufit |
| Get Number of Terms from bboufit_ml Object | nterms.bboufit_ml |
| Get Parameters from bboufit Object | pars.bboufit |
| Get Parameters from bboufit_ml Object | pars.bboufit_ml |
| Predict Recruitment | predict.bboufit_recruitment |
| Predict Survival | predict.bboufit_survival |
| Get Rhat of bboufit Object | rhat.bboufit |
| Get MCMC samples | samples samples.bboufit samples.bboufit_ml |
| Get Tidy Tibble from bboufit Object. | tidy.bboufit |
| Get Tidy Tibble from bboufit_ml Object. | tidy.bboufit_ml |
