R/priors.R

In poissonconsulting/bboutools: Boreal Caribou Survival, Recruitment and Population Growth

# Copyright 2022-2023 Integrated Ecological Research and Poisson Consulting Ltd.
# 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
#
# http://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.

priors_survival <- function() {
  c(
    b0_mu = 3,
    b0_sd = 10,
    bYear_mu = 0,
    bYear_sd = 2,
    bAnnual_sd = 10,
    sAnnual_rate = 1,
    sMonth_rate = 1
  )
}

priors_recruitment <- function() {
  c(
    b0_mu = -1,
    b0_sd = 5,
    bYear_mu = 0,
    bYear_sd = 2,
    bAnnual_sd = 5,
    sAnnual_rate = 1,
    adult_female_proportion_alpha = 65,
    adult_female_proportion_beta = 35
  )
}

#' Survival model default priors
#'
#' Prior distribution parameters and default values for survival model parameters.
#'
#' Intercept
#'
#' `b0 ~ Normal(mu = b0_mu, sd = b0_sd)`
#'
#' Year Trend
#'
#' `bYear ~ Normal(mu = bYear_mu, sd = bYear_sd)`
#'
#' Year fixed effect
#'
#' `bAnnual ~ Normal(mu = 0, sd = bAnnual_sd)`
#'
#' Standard deviation of annual random effect
#'
#' `sAnnual ~ Exponential(rate = sAnnual_rate)`
#'
#' Standard deviation of month random effect
#'
#' `sMonth ~ Exponential(rate = sMonth_rate)`
#'
#' @return A named vector.
#' @export
#'
#' @examples bb_priors_survival()
bb_priors_survival <- function() {
  priors_survival()
}

#' Recruitment model default priors
#'
#' Prior distribution parameters and default values for recruitment model parameters.
#'
#' Intercept
#'
#' `b0 ~ Normal(mu = b0_mu, sd = b0_sd)`
#'
#' Year Trend
#'
#' `bYear ~ Normal(mu = bYear_mu, sd = bYear_sd)`
#'
#' Year fixed effect
#'
#' `bAnnual ~ Normal(mu = 0, sd = bAnnual_sd)`
#'
#' Standard deviation of annual random effect
#'
#' `sAnnual ~ Exponential(rate = sAnnual_rate)`
#'
#' Adult female proportion
#'
#' `adult_female_proportion ~ Beta(alpha = adult_female_proportion_alpha, beta = adult_female_proportion_beta)`
#'
#' @return A named vector.
#' @export
#'
#' @examples bb_priors_survival()
bb_priors_recruitment <- function() {
  priors_recruitment()
}