R/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
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 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)

    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                 <- seq(sightingdata[1,1], test.year)

    sights              <- rep(0, times=length(yrs))

    res                 <- data.frame(yrs, sights)

    for(i in 1:length(sightingdata$yrs)){
       res$sights[length(seq(sightingdata$yrs[1], sightingdata$yrs[i]))] <- sightingdata$sights[i]

    }

    d1        <- which(res$sights>0)
    d2        <- d1[length(d1)]
    test.dat  <- res[(d2+1):length(res[,1]),]
    test.dat$chance <-0

    for(g in 1:length(test.dat$yrs)){
      dat      <-     res[res$yrs<=test.dat$yrs[g],]
      test.dat$chance[g] <-   Solow1993.eq2.fun(dat)
    }

    cut   <-   subset(test.dat, test.dat$chance<=alpha)
    fin   <-   data.frame(Estimate=cut$yrs[1])

      if(data.out==T){

      return(test.dat[,c(1,3)])

      }

    else{

      return(fin)
      }
  }