R/Rev_Solow93eq.R

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

#' Title
#'
#' @param sightingdata
#' @param alpha
#' @param test.year
#' @param data.out
#'
#' @return
#' @export
#'
#' @examples
Rev_Solow1993.eq2 <-
  function(sightingdata, alpha, test.year, data.out){

    ##some warnings

    ##data frame warnings
    if(missing(sightingdata))
      stop('missing data.frame', 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 data.frame 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)

    if(!is.numeric(test.year))
      stop('no "test.year" specified', call.=FALSE)

    if(missing(data.out))
      stop('data.out must be specified as either TRUE or FALSE', call.=FALSE)

    if(!is.logical(data.out))
      stop('data.out must be logical (TRUE or FALSE)', call.=FALSE)


    names(sightingdata) <- c("yrs", "sights")

    sightingdata        <- subset(sightingdata, sightingdata$sights > 0)
    yrs  <- sort(seq(sightingdata[1,1], test.year),decreasing = FALSE)
    data <- as.data.frame(yrs)
    data$chance <- NA

    for (i in 1:length(data$yrs)) {
      data$chance[i] <- Sol93_col(sightingdata,i + test.year -1)
    }

    if(data.out==T){

      return(data)

    }

    else{

      return(fin)
    }
  }