R/UD_SetNotFoundSpeciesTo0.R

In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

#' Set number of Not Found species to 0
#'
#' ADD DESCRIPTION
#'
#' @param densities
#' @param mb
#' @param meas
#' @param exp_design
#' @param compositions
#' @param species.tracked
#'
#' @importFrom dplyr filter distinct full_join
#'
#' @return
#'
#' @export
#'
#' @examples
SetNotFoundSpeciesTo0 <- function(
    densities,
    mb,
    meas,
    exp_design,
    compositions,
    species.tracked
    ){
  # create df that has all species tracked that could be there
  if(meas == "bemovi_mag_25_non_cropped") {
    mb <- mb %>% dplyr::filter(timestamp >= 20211103)
  }

temp <- apply(
    mb,
    1,
    function(row){
      timestamp <- row["timestamp"]
      bot <- row["bottle"]
      comp <- unlist(exp_design[exp_design$bottle==bot,"composition"])

      specs <- unlist(compositions[compositions$composition==comp,])
      specs <- names(which(specs==1))
      specs <- specs[tolower(specs) %in% tolower(species.tracked)]

      if(meas %in% c("bemovi_mag_25_cropped","bemovi_mag_25_non_cropped")) {
        specs <- c(specs,"Cryptomonas","Debris_and_other")
      }
      if (length(specs) > 0){
        df <- data.frame(
          timestamp=timestamp,
          bottle=bot,
          composition_id=comp,
          species=specs,
          row.names = NULL
        )
      } else {
        df <- NULL
      }
      return(df)
    }
  )
  temp <- do.call("rbind", temp) %>% dplyr::distinct()
  # set species that could be present but arent to 0
  densities <- dplyr::full_join(densities,temp) #any NAs?
  densities$density <- ifelse(is.na(densities$density),0,densities$density)
  return(densities)
}