R/check_inputs.R

In AIMS/NEC-estimation: A Bayesian No Effect Concentration (NEC) package. R package version 1. doi:10.5281/ZENODO.3966864

#    Copyright 2020 Australian Institute of Marine Science
#
#    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.

#' check_inputs
#'
#' Checks the input data for a jagsNEC model call
#'
#' @param  data a data.frame containing the data to use for the model
#'
#' @param x.var the column heading indicating the concentration (x) variable
#'
#' @param y.var the column heading indicating the response (y) variable
#'
#' @param trials.var the column heading indicating the column for the number of "trials" for binomial response data.
#' If not supplied, the model may run but will not be the model you intended!

check_inputs <- function(data,
                         x.var,
                         y.var,
                         trials.var) {
  # check the specified columns exist in data
  use.vars <- na.omit(c(y.var = y.var, x.var = x.var, trials.var))
  var.colms <- match(use.vars, colnames(data))
  missing.colms <- data.frame(val = use.vars[which(is.na(var.colms))], stringsAsFactors = FALSE)
  missing.colms$element <- rownames(missing.colms)
  if (length(na.omit(var.colms)) < length(use.vars)) {
    stop(paste("Your indicated ", paste(paste(missing.colms$element, " '", missing.colms$val, "'", sep = ""),
      collapse = ", "
    ),
    " is not present in your input data. Has this been mispecified?",
    sep = ""
    ))
  }

  # extract the data
  y.dat <- data[, y.var]
  x.dat <- data[, x.var]

  # check the x data are numeric
  if (class(x.dat) != "numeric") {
    stop(paste("Your indicated x.var column ", x.var, " contains data that is class ", class(x.dat), ".
                   The function jagsNEC requires the concentration data (argument x.var) to be numeric.", sep = ""))
  }

  # check data contains only finite values
  test.x <- mean(x.dat)
  test.y <- mean(y.dat)
  if (is.finite(test.x) != TRUE) {
    stop("Your x.var column contains values that are not finite.")
  }
  if (is.finite(test.y) != TRUE) {
    stop("Your y.var column contains values that are not finite.")
  }
}