bbousims

bbousims is a package to simulate Boreal Caribou population abundance over time from survival, ageing and birth processes. Survival and recruitment data from hypothetical composition surveys and collaring are simulated from key sampling parameters.

The output of bbs_simulate_caribou() is intended to be used as input data for bboutools functions for fitting survival and recruitment models and predicting population growth.

In addition, there is more general functionality for simulating population abundance given any set of stages, period duration, and survival, ageing and birth process matrices.

Installation

You can install the development version of bbousims from GitHub with:

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

Introduction

Simulate survival and fecundity rates

Simulate survival rates for each month, year and stage and fecundity rates for each year and stage. Rates are generated for female stages (female calf, female yearling and female adult). Female calf and female adult survival rates are specified from separate linear models, whereas female yearling survival is specified as an effect on female adult survival.

set.seed(1)
survival <- bbs_survival_caribou(
  survival_adult_female = 0.85,
  annual_sd_adult_female = 0.2,
  trend_adult_female = -0.1,
  month_sd_adult_female = 0.1,
  survival_calf_female = 0.5,
  yearling_effect = 0.05,
  nyear = 5
)

fecundity <- bbs_fecundity_caribou(
  calves_per_adult_female = 0.7,
  annual_sd = 0.1,
  nyear = 5
)

View expected monthly survival rates (‘eSurvival’) for adult females (stage 3) by each month and year.

survival$eSurvival[, , 3]
#>            [,1]      [,2]      [,3]      [,4]      [,5]
#>  [1,] 0.9834999 0.9844767 0.9790802 0.9856860 0.9797460
#>  [2,] 0.9854934 0.9863539 0.9815977 0.9874188 0.9821849
#>  [3,] 0.9858478 0.9866875 0.9820455 0.9877267 0.9826186
#>  [4,] 0.9856192 0.9864723 0.9817566 0.9875280 0.9823388
#>  [5,] 0.9843153 0.9852446 0.9801095 0.9863948 0.9807433
#>  [6,] 0.9868873 0.9876661 0.9833596 0.9886298 0.9838915
#>  [7,] 0.9853533 0.9862219 0.9814206 0.9872969 0.9820133
#>  [8,] 0.9838201 0.9847783 0.9794844 0.9859644 0.9801376
#>  [9,] 0.9810780 0.9821956 0.9760254 0.9835796 0.9767862
#> [10,] 0.9863772 0.9871859 0.9827146 0.9881866 0.9832668
#> [11,] 0.9847123 0.9856185 0.9806110 0.9867400 0.9812291
#> [12,] 0.9847556 0.9856591 0.9806656 0.9867775 0.9812819

Project population

Population is projected from survival and fecundity rates. Survival occurs at the end of each month and survival, ageing and birth occur at the end of each year, in that order.

Initial population abundance for each stage is determined from the initial number of adult females set by the user and the calculated stable stage distribution (see bbs_demographic_summary() for details). Population abundance for male stages are based on user-provided sex ratios.

set.seed(1)
population <- bbs_population_caribou(survival,
  fecundity = fecundity,
  adult_females = 500,
  proportion_adult_female = 0.65
)

The output is a matrix with abundance for each period and stage. The first period is the initial population and period 13 is the final month of the first year.

# projected population for first year
population[, 1:13]
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> [1,]  177  169  155  142  138  129  122  116  112   107   102    97   180
#> [2,]  163  167  143  138  142  138  119  128  108   114   120   101   180
#> [3,]   97   96   96   94   94   93   91   89   87    86    84    83    94
#> [4,]   96   93  104  102   91  102   90   99   96    84    93    76    97
#> [5,]  500  491  480  473  469  460  447  436  432   429   424   418   492
#> [6,]  263  257  273  237  239  259  238  245  225   252   234   228   271

Simulate abundance, survival and recruitment data

Abundance, survival and recruitment data are simulated from hypothetical composition surveys and collaring, given the survival and fecundity rates used to project the population and a set of key sampling parameters. The output is a list of lists of the abundance, survival, and recruitment data.frames for each simulation.

set.seed(1)
data <- bbs_simulate_caribou(
  survival = survival,
  fecundity = fecundity,
  nsims = 10,
  adult_females = 500,
  proportion_adult_female = 0.65,
  month_composition = 9L,
  collared_adult_females = 30,
  group_size = 6,
  group_coverage = 0.3
)

View collar survival data for the first simulation

# collar survival data for first simulation
print(data[[1]]$survival)
#> # A tibble: 60 × 6
#>     Year Month PopulationName StartTotal MortalitiesCertain MortalitiesUncertain
#>    <int> <int> <chr>               <dbl>              <int>                <int>
#>  1     1     1 A                      30                  1                    0
#>  2     1     2 A                      29                  0                    0
#>  3     1     3 A                      29                  2                    0
#>  4     1     4 A                      27                  1                    0
#>  5     1     5 A                      26                  0                    0
#>  6     1     6 A                      26                  0                    0
#>  7     1     7 A                      26                  1                    0
#>  8     1     8 A                      25                  0                    0
#>  9     1     9 A                      25                  0                    0
#> 10     1    10 A                      25                  0                    0
#> # ℹ 50 more rows

Work with bboutools

The survival and recruitment data.frames in the output of bbs_simulate_caribou() are intended to be used as input data for model fitting functions in the bboutools package.

# fit model for each simulation
# we set year_start = 1 because we assume the projected population is for the biological year
fits <- lapply(1:length(data), function(x) {
  survival <- data[[x]]$survival
  bboutools::bb_fit_survival(data = survival, year_start = 1L)
})

Information

Additional information is available from the bbousims website, including more in-depth articles:
- Get Started with bbousims.
- Work with bboutools.
- General tools (beyond Boreal Caribou).

bbou Suite

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

License

The code is released under the Apache License 2.0

Copyright 2024 Province of Alberta

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

https://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.