R/censor.R

In ssdtools: Species Sensitivity Distributions

#    Copyright 2021 Province of British Columbia
#
#    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.

.is_censored <- function(x) {
  !identical(x, c(0, Inf))
}

censoring_text <- function(x) {
  if(!.is_censored(x)) return(NULL)
  if(identical(x, c(NA_real_, NA_real_)))
    return("inconsistently censored")
  left <- if(x[1] == 0) NULL else paste0("left (", signif(x[1], 4), ")")
  right <- if(is.infinite(x[2])) NULL else paste0("right (", signif(x[2], 4), ")")
  censoring <- c(left, right)
  censoring <- cc(censoring, conj = " and ", brac = "")
  censoring <- paste0(censoring, " censored")
  censoring
}

#' Is Censored
#'
#' Deprecated for [`ssd_is_censored()`].
#' 
#' @param x A fitdists object.
#'
#' @return A flag indicating if the data is censored.
#' @export
#' @seealso [`ssd_is_censored()`]
#'
#' @examples
#' fits <- ssd_fit_dists(ssddata::ccme_boron)
#' is_censored(fits)
is_censored <- function(x) {
  deprecate_soft("0.3.7", "is_censored()", "ssd_is_censored()")
  chk_s3_class(x, "fitdists")
  ssd_is_censored(x)
}

censor_data <- function(data, censoring) {
  if(!.is_censored(censoring)) return(data)
  chk_not_any_na(censoring)
  
  data$left[data$left < censoring[1]] <- 0
  data$right[data$right > censoring[2]] <- Inf
  data
}

censoring <- function(data) {
  censoring <- c(0, Inf)
  data <- data[data$left != data$right,]
  
  if(!nrow(data))
    return(censoring)
  
  left <- data$left == 0
  right <- is.infinite(data$right)
  
  if(any(!left & !right)) return(c(NA_real_, NA_real_))
  
  censoring[1] <- max(0, data$right[data$left == 0])
  censoring[2] <- min(Inf, censoring[2], data$left[is.infinite(data$right)])
  
  if(censoring[1] >= censoring[2])
    return(c(NA_real_, NA_real_))
  
  censoring
}