R/bcanz.R

In ssdtools: Species Sensitivity Distributions

#    Copyright 2021 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.
#    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.

#' BCANZ Distributions
#' 
#' Gets a character vector of the names of the distributions
#' adopted by BC, Canada, Australia and New Zealand for official guidelines.
#'
#' @return A unique, sorted character vector of the distributions.
#' @seealso [`ssd_dists()`]
#' @family dists BCANZ
#' @export
#'
#' @examples
#' ssd_dists_bcanz()
ssd_dists_bcanz <- function() {
  ssd_dists(bcanz = TRUE)
}

#' Fit BCANZ Distributions
#'
#' Fits distributions using settings adopted by 
#' BC, Canada, Australia and New Zealand for official guidelines.
#'
#' @inheritParams params
#' @return An object of class fitdists.
#' @seealso [`ssd_fit_dists()`]
#' @family BCANZ
#' @export
#' @examples
#' ssd_fit_bcanz(ssddata::ccme_boron)
ssd_fit_bcanz <- function(data, left = "Conc") {
  ssd_fit_dists(data, 
                left = left,
                dists = ssd_dists_bcanz(),
                nrow = 6L,
                rescale = TRUE,
                reweight = FALSE,
                computable = TRUE,
                at_boundary_ok = FALSE, 
                min_pmix = 0) 
}

#' BCANZ Hazard Concentrations
#'
#' Gets hazard concentrations with confidence intervals that protect 
#' 1, 5, 10 and 20% of species using settings adopted by 
#' BC, Canada, Australia and New Zealand for official guidelines.
#' This function can take several minutes to run with required 10,000 iterations.
#'
#' @inheritParams params
#' @return A tibble of corresponding hazard concentrations.
#' @seealso [`ssd_hc()`].
#' @family BCANZ
#' @export
#' @examples
#' fits <- ssd_fit_bcanz(ssddata::ccme_boron)
#' ssd_hc_bcanz(fits, nboot = 100)
ssd_hc_bcanz <- function(x, nboot = 10000, delta = 10, min_pboot = 0.9) {
  ssd_hc(x, 
         percent = c(1,5,10,20), 
         ci = TRUE, 
         level = 0.95, 
         nboot = nboot, 
         average = TRUE, 
         delta = delta, 
         min_pboot = min_pboot, 
         parametric = TRUE)
}