R/test.breaks.R

In DistanceDevelopment/mrds: Mark-Recapture Distance Sampling

#' Test validity for histogram breaks(cutpoints)
#'
#' Determines whether user specified breaks for histograms are properly ordered
#' and match the left and right truncation.
#'
#' @param breaks vector of cutpoints (breaks) for distance histogram
#' @param left left truncation value
#' @param width right truncation value; either radius of point count or
#'   half-width of transect
#' @return vector of breaks modified to be valid if necessary
#' @author Jeff Laake
test.breaks <- function(breaks, left, width){

  # Make sure break points are in order
  if(any(breaks!=sort(breaks))){
    stop("Break points are out of order.")
  }

  # if any endpoint > width, issue warning and reset endpoints
  if(any(breaks>1.000001*width)){
    message(paste0("Specified endpoints > ", width, "; values reset."))
    breaks <- c(breaks[breaks<width], width)
  }

  # if last endpoint does not include width reset last endpoint
  if(breaks[length(breaks)]<0.999999*width){
    message(paste0("Last interval endpoint did not include ", width,
                   ". It was reset."))
    breaks <- c(breaks, width)
  }

  # if any endpoint < left, issue warning and reset endpoints
  if(any(breaks<0.99999*left)){
    message(paste0("Specified endpoints < ", left, "; values reset."))
    breaks <- c(left, breaks[breaks>left])
  }

  # if first endpoint does not include left reset last first point
  if(breaks[1]>1.00001*left){
    message(paste0("First interval endpoint did not include ", left,
                   ". It was reset"))
    breaks <- c(left, breaks)
  }
  return(breaks)
}