R/missing.specimens.R

In LOST: Missing Morphometric Data Simulation and Estimation

missing.specimens <-
function (dataset, nspremove, nldremove, nlandmarks) 
{
  remove.coor.random <- function(single, j, nlandmarks) {
    nld <- 1:nlandmarks
    r <- sample(nld, j)
    for (m in 1:j) {
      d <- r[m]
      single[d, ] <- rep(NA, ncol(single))
    }
    return(single)
  }
  nspecimen <- nrow(dataset)/nlandmarks
  start <- seq(from = 1, to = nrow(dataset), by = nlandmarks)
  nsp <- 1:nspecimen
  removes <- sample(nsp, nspremove)
  for (k in 1:nspremove) {
    specimen <- removes[k]
    x <- start[specimen]
    y <- x + nlandmarks - 1
    single <- dataset[x:y, ]
    j <- sample(nldremove, 1)
    newsingle <- remove.coor.random(single, j, nlandmarks)
    dataset[x:y, ] <- newsingle
  }
  return(dataset)
}