R/OLEeq.R

In Clara-Casabona/ExtinctModels: Models to infer the date of extinction

#' OLE
#'
#' @param sightingdata
#' @param alpha
#'
#' @return
#' @export
#'
#' @examples
OLE <-
  function(sightingdata, alpha){

    ##some warnings

    ##data frame warnings
    if(missing(sightingdata))
      stop('no data present', call.=FALSE)

    if(!is.numeric(sightingdata[,1]))
      stop('sighting data must be a data.frame of real numbers', call.=FALSE)

    if(!is.numeric(sightingdata[,2]))
      stop('sighting data must be a dataframe of real numbers', call.=FALSE)

    if(ncol(sightingdata)<2)
      stop('some data missing', call.=FALSE)

    if(max(sightingdata[,2])>max(sightingdata[,1]))
      warning("Check column values are correct, values for number of sighting events appear to be larger than the years at which sightings occur", call.=FALSE)

    if(ncol(sightingdata)>2)
      warning("data passed to the function is larger than 2 columns, extinction is being estimated from the values in the first two columns only", call.=FALSE)

    if(min(sightingdata[,2])<0)
      stop('sightingdata cannot contain negative values', call.=FALSE)

    if(min(sightingdata[,1])<0)
      stop('sightingdata cannot contain negative values', call.=FALSE)

    if(min(diff(sightingdata[,1]))==0)
      stop('multiple identical year values entered', call.=FALSE)

    if(min(diff(sightingdata[,1]))<0)
      warning("sightingdata has been ordered by the time column", call.=FALSE)

    if(min(diff(sightingdata[,1]))<0)
      sightingdata<-sightingdata[order(sightingdata[,1]),]

    ##missing value warnings
    if(missing(alpha))
      stop('no alpha value specified', call.=FALSE)

    if(alpha>1)
      stop('alpha value must be less than 1', call.=FALSE)

    if(alpha<0)
      stop('alpha value must be a positive number', call.=FALSE)

    OLE.fun(sightingdata, alpha)
  }