| Title: | Data for bbou Project |
|---|---|
| Description: | This package contains boreal caribou demographic data which can be used as validation for the associated shiny-app and analysis. The overall goal of the bbou packages is to develop a more standardized and consistent method for the comparison of boreal caribou survival rates, recruitment and population dynamics across Canada. |
| Authors: | Troy Hegel [aut], Dave Hervieux [aut], Barry Nobert [aut], John Boulanger [aut] (ORCID: <https://orcid.org/0000-0001-8222-1445>), Ayla Pearson [aut, cre] (ORCID: <https://orcid.org/0000-0001-7388-1222>), Joe Thorley [ctb] (ORCID: <https://orcid.org/0000-0002-7683-4592>), Seb Dalgarno [ctb] (ORCID: <https://orcid.org/0000-0002-3658-4517>), Alan Constant [ctb] (ORCID: <https://orcid.org/0000-0002-1652-4031>), Josie Hughes [ctb] (Multi-population and other extensions based on LandSciTech/bboudata), Province of Alberta [cph], His Majesty the King in Right of Canada, as represented by the Minister of the Environment [cph] (Copyright applies to bbd_chk_data_survival(), bbd_chk_data_recruitment(), and associated helpers in R/functions.R, derived from LandSciTech/bboudata) |
| Maintainer: | Ayla Pearson <[email protected]> |
| License: | Apache License (>= 2) |
| Version: | 0.4.0 |
| Built: | 2026-06-05 19:50:34 UTC |
| Source: | https://github.com/poissonconsulting/bboudata |
The data must follow all requirements to not error. This format is required for usage of the bbou suite of tools.
bbd_chk_data_recruitment( data, x_name = deparse(substitute(data)), multi_population = FALSE, allow_missing = FALSE )bbd_chk_data_recruitment( data, x_name = deparse(substitute(data)), multi_population = FALSE, allow_missing = FALSE )
data |
The data.frame to check. |
x_name |
A string of the name of the data.frame. |
multi_population |
A flag indicating whether to accept multiple populations. |
allow_missing |
A flag indicating whether to accept placeholder rows for unobserved years. When TRUE, rows with all-NA measurement columns (Month, Day, Cows, Bulls, UnknownAdults, Yearlings, Calves) are permitted. These rows signal unobserved years to the model. |
The data must follow the requirements:
Name of the herd or population
The calendar year the observation occurred. Must be a positive integer.
The calendar month the observation occurred. Must be an integer between 1 and 12.
The day the observation occurred. Must be an integer between 1 and 31.
The total number of cows counted in each group in a survey/year. Must be a positive integer.
The total number of bulls counted in each group in a survey/year. Must be a positive integer
The total number of adults counted that the sex could not be identified in each group in a survey/year. Must be a positive integer.
The total number of yearlings that did not have the sex identified in each group in a survey/year. Must be a positive integer.
The total number of calves counted in each group in a survey/year. Must be a positive integer.
An invisible copy of the original data.frame.
bbd_chk_data_recruitment(bbourecruit_a) bbd_chk_data_recruitment(bbourecruit_b) bbd_chk_data_recruitment(bbourecruit_c) # this example will error as it doesn't follow the requirements x <- bbourecruit_a x[1, 4] <- 32L try(bbd_chk_data_recruitment(x))bbd_chk_data_recruitment(bbourecruit_a) bbd_chk_data_recruitment(bbourecruit_b) bbd_chk_data_recruitment(bbourecruit_c) # this example will error as it doesn't follow the requirements x <- bbourecruit_a x[1, 4] <- 32L try(bbd_chk_data_recruitment(x))
The data must follow all requirements to not error. This format is required for usage of the bbou suite of tools.
bbd_chk_data_survival( data, x_name = deparse(substitute(data)), multi_population = FALSE, allow_missing = FALSE )bbd_chk_data_survival( data, x_name = deparse(substitute(data)), multi_population = FALSE, allow_missing = FALSE )
data |
The data.frame to check. |
x_name |
A string of the name of the data.frame. |
multi_population |
A flag indicating whether to accept multiple populations. |
allow_missing |
A flag indicating whether to accept placeholder rows for unobserved years. When TRUE, rows with all-NA measurement columns (Month, StartTotal, MortalitiesCertain, MortalitiesUncertain) are permitted. These rows signal unobserved years to the model. |
The data must follow the requirements:
Name of the herd or population
The calendar year the observation occurred. Must be a positive integer.
The calendar month the observation occurred. Must be an integer between 1 and 12.
The total number of collared caribou at the start of the month. Must be a positive integer.
The total number of confirmed mortalities in that month. Must be a positive integer.
The total number of mortalities that were not confirmed in that month. Must be a positive integer.
An invisible copy of the original data.frame.
bbd_chk_data_survival(bbousurv_a) bbd_chk_data_survival(bbousurv_b) bbd_chk_data_survival(bbousurv_c) # this example will error as it doesn't follow the requirements x <- bbousurv_c x[1, 3] <- 14L try(bbd_chk_data_survival(x))bbd_chk_data_survival(bbousurv_a) bbd_chk_data_survival(bbousurv_b) bbd_chk_data_survival(bbousurv_c) # this example will error as it doesn't follow the requirements x <- bbousurv_c x[1, 3] <- 14L try(bbd_chk_data_survival(x))
The data contains anonymized recruitment information for boreal caribou population 'A', which spans 27 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using calf/cow age ratios.
bbourecruit_abbourecruit_a
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized recruitment information for boreal caribou population 'B' which spans 15 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using calf/cow age ratios.
bbourecruit_bbbourecruit_b
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized recruitment information for boreal caribou population 'C', which spans 9 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using calf/cow age ratios.
bbourecruit_cbbourecruit_c
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized recruitment information for boreal caribou population 'C', with years 2010-2013 represented as single placeholder rows with all-NA measurement columns. These placeholder rows signal unobserved years to the model: the data pipeline uses them to set Annual factor levels, then strips them before building the likelihood. Random effects for unobserved years are estimated purely from the hierarchical prior. The dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using calf/cow age ratios.
bbourecruit_missingbbourecruit_missing
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized recruitment information for boreal caribou populations 'A', 'B' and 'C' with staggered year ranges, an internal gap (B missing 2009-2010), and unobserved year placeholder rows (2016 for all populations). Designed to test multi-population analysis, latent random effects for missing year-population combos, and unobserved year prediction. Filter to single population or remove placeholder rows (where Month is NA) as needed. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using calf/cow age ratios.
bbourecruit_multibbourecruit_multi
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a stable population spanning 20 years with annual variation on
female adult survival and female calf survival. Coverage is low, with 20% of groups observed and 10 collars.
This dataset follows the methodology described in DeCesare et al. (2012) for estimating
population growth rates using calf/cow age ratios.
bbourecruit_sim1bbourecruit_sim1
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a stable population spanning 20 years with annual variation on
female adult survival and female calf survival. Coverage is high, with 70% of groups observed and 40 collars.
This dataset follows the methodology described in DeCesare et al. (2012) for estimating
population growth rates using calf/cow age ratios.
bbourecruit_sim2bbourecruit_sim2
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a population spanning 20 years with negative trend on female adult survival
and additional annual variation on female adult survival and female calf survival.
Coverage is medium, with 50% of groups observed and 25 collars.
This dataset follows the methodology described in DeCesare et al. (2012) for estimating
population growth rates using calf/cow age ratios.
bbourecruit_sim3bbourecruit_sim3
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a stable population spanning 20 years with small population size
(50 initial adult females) and annual variation on female adult survival and female calf survival.
Coverage is medium, with 40% of groups observed and 20 collars.
This dataset follows the methodology described in DeCesare et al. (2012) for estimating
population growth rates using calf/cow age ratios.
bbourecruit_sim4bbourecruit_sim4
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The day the observation occurred
The number of cows counted in the group
The number of bulls counted in the group
The number of adults which could not be sexed in the group
The number of yearlings counted in the group
The number of calves counted in the group
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou population 'A', which spans 31 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_abbousurv_a
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou populations 'A' and 'C', aggregated to annual resolution with staggered year ranges. Designed to test the combination of multi-population analysis with aggregate annual data. Filter to single population for simple annual-only testing. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_annualbbousurv_annual
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou population 'B', which spans 18 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_bbbousurv_b
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou population 'C', which spans 11 years. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_cbbousurv_c
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou population 'C', with years 2010-2013 represented as single placeholder rows with all-NA measurement columns. These placeholder rows signal unobserved years to the model: the data pipeline uses them to set Annual factor levels, then strips them before building the likelihood. Random effects for unobserved years are estimated purely from the hierarchical prior. The dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_missingbbousurv_missing
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
The data contains anonymized survival information for boreal caribou populations 'A', 'B' and 'C' with staggered year ranges, an internal gap (B missing 2008-2009), and unobserved year placeholder rows (2015 for all populations). Designed to test multi-population analysis, latent random effects for missing year-population combos, and unobserved year prediction. Filter to single population or remove placeholder rows (where Month is NA) as needed. This dataset follows the methodology described in DeCesare et al. (2012) for estimating population growth rates using adult female survival data.
bbousurv_multibbousurv_multi
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
The data is released under the Open Government Licence - Alberta
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with the bbousims package.
This is a stable population spanning 20 years with annual variation on
female adult survival and female calf survival.
Coverage is low, with 20% of groups observed and 10 collars.
The dataset follows methodology described in DeCesare et al. (2012) for estimating
population growth rates using adult female survival data.
bbousurv_sim1bbousurv_sim1
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a stable population spanning 20 years with annual variation on
female adult survival and female calf survival.
Coverage is high, with 70% of groups observed and 40 collars.
The dataset follows methodology described in DeCesare et al. (2012) for estimating
population growth rates using adult female survival data.
bbousurv_sim2bbousurv_sim2
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a population spanning 20 years with negative trend on female adult survival
and additional annual variation on female adult survival and female calf survival.
Coverage is medium, with 50% of groups observed and 25 collars.
The dataset follows methodology described in DeCesare et al. (2012) for estimating
population growth rates using adult female survival data.
bbousurv_sim3bbousurv_sim3
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244
Data are simulated with bbousims package.
This is a stable population spanning 20 years with small population size
(50 initial adult females) and annual variation on female adult survival and female calf survival.
Coverage is medium, with 40% of groups observed and 20 collars.
The dataset follows methodology described in DeCesare et al. (2012) for estimating
population growth rates using adult female survival data.
bbousurv_sim4bbousurv_sim4
A tibble with columns:
Name of the population
The year the observation occurred
The month the observation occurred
The total number of collared caribou at the start of the month
The number of confirmed caribou mortalities in the month
The total number of mortalities that were not confirmed in that month
DeCesare, N.J., Hebblewhite, M., Bradley, M., Smith, K.G., Hervieux, D., & Neufeld, L. (2012). Estimating ungulate recruitment and growth rates using age ratios. The Journal of Wildlife Management, 76(1), 144-153. doi:10.1002/jwmg.244