poissonconsulting · sebdalgarno · Nov 13, 2025 · Nov 13, 2025 · Nov 13, 2025 · Nov 13, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,5 @@
 ^_pkgdown\.yml$
 ^README\.Rmd$
 ^CODE_OF_CONDUCT\.md$
+^\.claude$
+^CLAUDE\.md$
diff --git a/.gitignore b/.gitignore
@@ -18,3 +18,6 @@ output[0-9]/
 output-20[0-9][0-9]-[0-9][0-9]*
 
 report/
+
+.claude/
+CLAUDE.md
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: bboudata
 Title: Data for bbou Project
-Version: 0.3.2
+Version: 0.4.0
 Authors@R: c(
     person("Troy", "Hegel", , "troy.hegel@gov.ab.ca", role = "aut"),
     person("Dave", "Hervieux", , "dave.hervieux@gov.ab.ca", role = "aut"),
@@ -28,7 +28,7 @@ URL: https://poissonconsulting.github.io/bboudata/,
     https://github.com/poissonconsulting/bboudata
 BugReports: https://github.com/poissonconsulting/bboudata/issues
 Depends:
-    R (>= 3.4)
+    R (>= 4.1)
 Imports:
     chk,
     tibble
@@ -41,5 +41,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2.9000
+RoxygenNote: 7.3.3.9000
 Config/Needs/website: poissonconsulting/poissontemplate
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,17 @@
-<!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
+# bboudata 0.4.0
+
+Updated for bboutools 1.3.0.
+
+## New features
+
+* `bbd_chk_data_survival()` and `bbd_chk_data_recruitment()` gained `multi_population` and `allow_missing` arguments to support multi-population data and unobserved year placeholder rows.
+* `bbd_chk_data_survival()` and `bbd_chk_data_recruitment()` now validate that placeholder rows have all measurement columns as NA (not just some) when `allow_missing = TRUE` (#94).
+
+## Datasets
+
+* Added `bbousurv_multi` and `bbourecruit_multi` — multi-population datasets (populations A, B, C) with staggered year ranges, an internal data gap, and unobserved year placeholder rows.
+* Added `bbousurv_missing` and `bbourecruit_missing` — single-population (C) datasets with unobserved year placeholder rows.
+* Added `bbousurv_annual` — multi-population (A, C) aggregate annual survival data with staggered years.
 
 # bboudata 0.3.2
 

diff --git a/R/bbourecruit.R b/R/bbourecruit.R
@@ -1,5 +1,6 @@
 # Copyright 2022-2023 Integrated Ecological Research and Poisson Consulting Ltd.
 # Copyright 2024 Province of Alberta
+# Copyright 2025 Environment and Climate Change Canada
 #
 # Licensed under the Apache License, Version 2.0 (the 'License');
 # you may not use this file except in compliance with the License.
@@ -43,6 +44,75 @@
 #'
 "bbourecruit_a"
 
+#' Sample Data for Multiple Populations
+#'
+#' 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.
+#'
+#' @details The data is released under the [Open Government Licence -
+#' Alberta](https://open.alberta.ca/licence)
+#'
+#' @references
+#' 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
+#'
+#' @format A tibble with columns:
+#' \describe{
+#' \item{PopulationName}{Name of the population}
+#' \item{Year}{The year the observation occurred}
+#' \item{Month}{The month the observation occurred}
+#' \item{Day}{The day the observation occurred}
+#' \item{Cows}{The number of cows counted in the group}
+#' \item{Bulls}{The number of bulls counted in the group}
+#' \item{UnknownAdults}{The number of adults which could not be sexed in the
+#' group}
+#' \item{Yearlings}{The number of yearlings counted in the group}
+#' \item{Calves}{The number of calves counted in the group}
+#' }
+#'
+"bbourecruit_multi"
+
+#' Sample Data with Unobserved Years
+#'
+#' 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.
+#'
+#' @details The data is released under the [Open Government Licence -
+#' Alberta](https://open.alberta.ca/licence)
+#'
+#' @references
+#' 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
+#'
+#' @format A tibble with columns:
+#' \describe{
+#' \item{PopulationName}{Name of the population}
+#' \item{Year}{The year the observation occurred}
+#' \item{Month}{The month the observation occurred}
+#' \item{Day}{The day the observation occurred}
+#' \item{Cows}{The number of cows counted in the group}
+#' \item{Bulls}{The number of bulls counted in the group}
+#' \item{UnknownAdults}{The number of adults which could not be sexed in the
+#' group}
+#' \item{Yearlings}{The number of yearlings counted in the group}
+#' \item{Calves}{The number of calves counted in the group}
+#' }
+#'
+"bbourecruit_missing"
+
 #' Sample Data for Population B
 #'
 #' The data contains anonymized recruitment information for boreal caribou population 'B'

diff --git a/R/bbousurv.R b/R/bbousurv.R
@@ -1,5 +1,6 @@
 # Copyright 2022-2023 Integrated Ecological Research and Poisson Consulting Ltd.
 # Copyright 2024 Province of Alberta
+# Copyright 2025 Environment and Climate Change Canada
 #
 # Licensed under the Apache License, Version 2.0 (the 'License');
 # you may not use this file except in compliance with the License.
@@ -103,6 +104,107 @@
 #'
 "bbousurv_c"
 
+#' Sample Data for Multiple Populations
+#'
+#' 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.
+#'
+#' @details
+#' The data is released under the [Open Government Licence -
+#' Alberta](https://open.alberta.ca/licence)
+#'
+#' @references
+#' 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
+#'
+#' @format A tibble with columns:
+#' \describe{
+#' \item{PopulationName}{Name of the population}
+#' \item{Year}{The year the observation occurred}
+#' \item{Month}{The month the observation occurred}
+#' \item{StartTotal}{The total number of collared caribou at the start of the
+#' month}
+#' \item{MortalitiesCertain}{The number of confirmed caribou mortalities in the
+#' month}
+#' \item{MortalitiesUncertain}{The total number of mortalities that were not
+#' confirmed in that month}
+#' }
+#'
+"bbousurv_multi"
+
+#' Sample Data for Annual Survival Data
+#'
+#' 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.
+#'
+#' @details
+#' The data is released under the [Open Government Licence -
+#' Alberta](https://open.alberta.ca/licence)
+#'
+#' @references
+#' 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
+#'
+#' @format A tibble with columns:
+#' \describe{
+#' \item{PopulationName}{Name of the population}
+#' \item{Year}{The year the observation occurred}
+#' \item{Month}{The month the observation occurred}
+#' \item{StartTotal}{The total number of collared caribou at the start of the
+#' month}
+#' \item{MortalitiesCertain}{The number of confirmed caribou mortalities in the
+#' month}
+#' \item{MortalitiesUncertain}{The total number of mortalities that were not
+#' confirmed in that month}
+#' }
+#'
+"bbousurv_annual"
+
+#' Sample Data with Unobserved Years
+#'
+#' 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.
+#'
+#' @details
+#' The data is released under the [Open Government Licence -
+#' Alberta](https://open.alberta.ca/licence)
+#'
+#' @references
+#' 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
+#'
+#' @format A tibble with columns:
+#' \describe{
+#' \item{PopulationName}{Name of the population}
+#' \item{Year}{The year the observation occurred}
+#' \item{Month}{The month the observation occurred}
+#' \item{StartTotal}{The total number of collared caribou at the start of the
+#' month}
+#' \item{MortalitiesCertain}{The number of confirmed caribou mortalities in the
+#' month}
+#' \item{MortalitiesUncertain}{The total number of mortalities that were not
+#' confirmed in that month}
+#' }
+#'
+"bbousurv_missing"
+
 #' Simulated Data for Scenario 1
 #'
 #' Data are simulated with the [`bbousims`](https://poissonconsulting.github.io/bbousims/) package.

diff --git a/R/chk-data-recruitment.R b/R/chk-data-recruitment.R
@@ -1,5 +1,6 @@
 # Copyright 2022-2023 Integrated Ecological Research and Poisson Consulting Ltd.
 # Copyright 2024 Province of Alberta
+# Copyright 2025 Environment and Climate Change Canada
 #
 # Licensed under the Apache License, Version 2.0 (the 'License');
 # you may not use this file except in compliance with the License.
@@ -40,10 +41,12 @@
 #' survey/year. Must be a positive integer.}
 #' }
 #'
-#' @param data The data frame check.
-#' @param x_name Name of data frame.
-#'
-#' @return An invisible copy of the original data frame.
+#' @param data The data.frame to check.
+#' @param x_name A string of the name of the data.frame.
+#' @param multi_population A flag indicating whether to accept multiple populations.
+#' @param 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.
+
+#' @return An invisible copy of the original data.frame.
 #' @export
 #'
 #' @examples
@@ -55,7 +58,11 @@
 #' x <- bbourecruit_a
 #' x[1, 4] <- 32L
 #' try(bbd_chk_data_recruitment(x))
-bbd_chk_data_recruitment <- function(data, x_name = deparse(substitute(data))) {
+bbd_chk_data_recruitment <- function(data, x_name = deparse(substitute(data)),
+                                     multi_population = FALSE, allow_missing = FALSE) {
+  chk::chk_flag(multi_population)
+  chk::chk_flag(allow_missing)
+
   nms <- c(
     "PopulationName", "Year", "Month", "Day", "Cows",
     "Bulls", "UnknownAdults", "Yearlings", "Calves"
@@ -64,35 +71,62 @@ bbd_chk_data_recruitment <- function(data, x_name = deparse(substitute(data))) {
 
   chk::chk_character_or_factor(data$PopulationName, x_name = xname(x_name, "PopulationName"))
   chk::chk_not_any_na(data$PopulationName, x_name = "PopulationName")
-  .chk_population(data)
+  if (!multi_population) {
+    .chk_single_population(data)
+  }
 
   chk::chk_whole_numeric(data$Year, x_name = xname(x_name, "Year"))
   chk::chk_gte(data$Year, 0, x_name = xname(x_name, "Year"))
 
-  chk::chk_whole_numeric(data$Month, x_name = xname(x_name, "Month"))
-  chk::chk_range(data$Month, range = c(1, 12), x_name = xname(x_name, "Month"))
-
-  chk::chk_whole_numeric(data$Day, x_name = xname(x_name, "Day"))
-  chk::chk_range(data$Day, range = c(1, 31), x_name = xname(x_name, "Day"))
-
   chk::chk_not_any_na(data$Year, x_name = "Year")
-  chk::chk_not_any_na(data$Month, x_name = "Month")
-  chk::chk_not_any_na(data$Day, x_name = "Day")
 
+  chk::chk_whole_numeric(data$Month, x_name = xname(x_name, "Month"))
+  chk::chk_whole_numeric(data$Day, x_name = xname(x_name, "Day"))
   chk::chk_whole_numeric(data$Cows, x_name = xname(x_name, "Cows"))
   chk::chk_gte(data$Cows, 0, x_name = xname(x_name, "Cows"))
-
   chk::chk_whole_numeric(data$Bulls, x_name = xname(x_name, "Bulls"))
   chk::chk_gte(data$Bulls, 0, x_name = xname(x_name, "Bulls"))
-
   chk::chk_whole_numeric(data$UnknownAdults, x_name = xname(x_name, "UnknownAdults"))
   chk::chk_gte(data$UnknownAdults, 0, x_name = xname(x_name, "UnknownAdults"))
-
   chk::chk_whole_numeric(data$Yearlings, x_name = xname(x_name, "Yearlings"))
   chk::chk_gte(data$Yearlings, 0, x_name = xname(x_name, "Yearlings"))
-
   chk::chk_whole_numeric(data$Calves, x_name = xname(x_name, "Calves"))
   chk::chk_gte(data$Calves, 0, x_name = xname(x_name, "Calves"))
 
+  if (!allow_missing) {
+    chk::chk_range(data$Month, range = c(1, 12), x_name = xname(x_name, "Month"))
+    chk::chk_not_any_na(data$Month, x_name = "Month")
+    chk::chk_range(data$Day, range = c(1, 31), x_name = xname(x_name, "Day"))
+    chk::chk_not_any_na(data$Day, x_name = "Day")
+    chk::chk_not_any_na(data$Cows, x_name = xname(x_name, "Cows"))
+    chk::chk_not_any_na(data$Bulls, x_name = xname(x_name, "Bulls"))
+    chk::chk_not_any_na(data$UnknownAdults, x_name = xname(x_name, "UnknownAdults"))
+    chk::chk_not_any_na(data$Yearlings, x_name = xname(x_name, "Yearlings"))
+    chk::chk_not_any_na(data$Calves, x_name = xname(x_name, "Calves"))
+  } else {
+    .chk_placeholder_all_or_nothing(
+      data,
+      c("Cows", "Bulls", "UnknownAdults", "Yearlings", "Calves")
+    )
+    placeholder <- is.na(data$Cows) &
+      is.na(data$Bulls) &
+      is.na(data$UnknownAdults) &
+      is.na(data$Yearlings) &
+      is.na(data$Calves)
+    if (any(placeholder) && !all(is.na(data$Month[placeholder]))) {
+      chk::abort_chk("Placeholder rows must have `Month` as NA.")
+    }
+    if (any(placeholder) && !all(is.na(data$Day[placeholder]))) {
+      chk::abort_chk("Placeholder rows must have `Day` as NA.")
+    }
+    if (any(!placeholder)) {
+      obs <- data[!placeholder, , drop = FALSE]
+      chk::chk_not_any_na(obs$Month, x_name = "Month")
+      chk::chk_range(obs$Month, range = c(1, 12), x_name = xname(x_name, "Month"))
+      chk::chk_not_any_na(obs$Day, x_name = "Day")
+      chk::chk_range(obs$Day, range = c(1, 31), x_name = xname(x_name, "Day"))
+    }
+  }
+
   invisible(data)
 }