Package: bboutools 0.1.0

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:Seb Dalgarno [aut, cre], Joe Thorley [aut], John Boulanger [aut], Ayla Pearson [aut], Environment and Climate Change Canada [cph]

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bboutools.pdf |bboutools.html✨
bboutools/json (API)
NEWS

# 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:https://poissonconsulting.github.io

On CRAN:

5.10 score 1 stars 2 packages 14 scripts 43 exports 53 dependencies

Last updated 2 months agofrom:e383ae601b. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 27 2024
R-4.5-win	OK	Nov 27 2024
R-4.5-linux	OK	Nov 27 2024
R-4.4-win	OK	Nov 27 2024
R-4.4-mac	OK	Nov 27 2024
R-4.3-win	OK	Nov 27 2024
R-4.3-mac	OK	Nov 27 2024

Exports:augment bb_fit_recruitment bb_fit_recruitment_ml bb_fit_survival bb_fit_survival_ml bb_plot_month bb_plot_month_survival bb_plot_year bb_plot_year_growth bb_plot_year_population_change bb_plot_year_recruitment bb_plot_year_survival bb_plot_year_trend_recruitment bb_plot_year_trend_survival bb_predict_calf_cow_ratio bb_predict_growth bb_predict_lambda bb_predict_population_change bb_predict_recruitment bb_predict_recruitment_trend bb_predict_survival bb_predict_survival_trend bb_priors_recruitment bb_priors_survival coef converged esr estimates glance logLik model_code model_recruitment model_survival nchains niters nobs npars nterms pars predict rhat samples tidy

Dependencies:abind bboudata chk cli coda colorspace cpp11 dplyr extras fansi farver generics ggplot2 glue gtable hms igraph isoband labeling lattice lifecycle magrittr MASS Matrix mcmcderive mcmcr mgcv munsell newdata nimble nlist nlme numDeriv pillar pkgconfig pracma purrr R6 RColorBrewer rescale rlang scales stringi stringr term tibble tidyr tidyselect universals utf8 vctrs viridisLite withr

Getting Started with bboutools

Rendered frombboutools.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2024-10-28
Started: 2024-04-27

Citation

Development and contributors

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 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 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 Population Growth Lambda	bb_predict_growth bb_predict_lambda
Predict Population Change	bb_predict_population_change
Predict Recruitment	bb_predict_recruitment
Predict Recruitment Trend	bb_predict_recruitment_trend
Predict Survival	bb_predict_survival
Predict Survival Trend	bb_predict_survival_trend
Recruitment model default priors	bb_priors_recruitment
Survival model default priors	bb_priors_survival
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