bbouretro

June 6, 2025 · View on GitHub

Introduction

The goal of bbouretro is to provide the ability to calculate survival, recruitment and population growth using the traditional methods.

Installation

To install the latest version from GitHub

# install.packages("remotes")
remotes::install_github("poissonconsulting/bbouretro")

Example

set.seed(101)

library(bbouretro)
library(bboudata)
#> 
#> Attaching package: 'bboudata'
#> The following object is masked from 'package:bbouretro':
#> 
#>     licensing_md

# generate recruitment estimate for each year
recruitment_est <-
  bbr_recruitment(
    bboudata::bbourecruit_c,
    adult_female_proportion = 0.65,
    sex_ratio = 0.5,
    variance = "bootstrap"
  )
bbr_plot_recruitment(recruitment_est)


# generate survival estimate for each year
survival_est <-
  bbr_survival(
    bboudata::bbousurv_c,
    include_uncertain_morts = TRUE,
    variance = "greenwood"
  )
bbr_plot_survival(survival_est)


# calculate lambda now that both recruitment and survival have been calculated
growth_est <- bbr_growth(survival_est, recruitment_est)
summary <- bbr_growth_summarize(growth_est)
summary
#> # A tibble: 9 × 13
#>   PopulationName CaribouYear     S     R estimate     se  lower  upper prop_lgt1
#>   <chr>                <int> <dbl> <dbl>    <dbl>  <dbl>  <dbl>  <dbl>     <dbl>
#> 1 C                     2004 0.867 0.096    0.959  0.115  0.636  1.08      0.323
#> 2 C                     2005 0.832 0.08     0.904  0.105  0.633  1.03      0.093
#> 3 C                     2006 1     0.068    1.07  NA     NA     NA        NA    
#> 4 C                     2007 0.458 0.059    0.487  0.128  0.262  0.766     0    
#> 5 C                     2008 0.941 0.083    1.03   0.1    0.739  1.16      0.615
#> 6 C                     2009 1     0.14     1.16  NA     NA     NA        NA    
#> 7 C                     2010 0.926 0.158    1.1    0.085  0.877  1.23      0.854
#> 8 C                     2011 0.96  0.112    1.08   0.075  0.872  1.16      0.861
#> 9 C                     2012 0.924 0.133    1.07   0.072  0.875  1.15      0.808
#> # ℹ 4 more variables: mean_sim_survival <dbl>, mean_sim_recruitment <dbl>,
#> #   mean_sim_growth <dbl>, median_sim_growth <dbl>
bbr_plot_growth(growth_est)

bbr_plot_growth_distributions(growth_est)

bbou Suite

bbouretro is part of the bbou suite of tools. Other packages in this suite include:

Contribution

Please report any issues.

Pull requests are always welcome.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Licensing

The documentation is released under the CC BY 4.0 License

The code is released under the Apache License 2.0