bbouretro

Introduction

The goal of bbouretro is to provide the ability to calculate survival, recruitment and population growth using the classical 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)

# generate recruitment estimate for each year
recruitment_est <-
  bbr_recruitment(
    bboudata::bbourecruit_c,
    p_females = 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,
    mort_type = "total",
    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:

• bboudata
• bboutools
• bboushiny
• bbousims

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.