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#' for individuals of known origin in the mixture, put all their weight on their known collection
#'
#' This is used internally.
#' @param SL the matrix of scaled likelihoods.
#' @param KC a character vector of collections that the individuals belong to (or NA if you
#' don't know where they come from). If this is NULL, then SL just gets returned untouched.
#' @param CFL the levels of the collections factor (which is within clean$short)
#' @export
#' @keywords internal
modify_scaled_likelihoods_for_known_mixture_fish <- function(SL, KC, CFL) {
# if there is no known collection column, just return SL untouched
if(is.null(KC)) {
return(SL)
}
ret <- SL
# otherwise, do what needs to be done
ipops <- as.integer(factor(KC, levels = CFL))
for(i in 1:ncol(SL)) {
if(!is.na(ipops[i])) {
ret[, i] <- 1e-100 # putting this in here in case we end up taking logs of it or something. (1 over a googol is close to 0...)
ret[ipops[i], i] <- 1.0
}
}
ret
}
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