R/makeTangle.R

In robschick/tangled: Creates data objects and plots for Knowlton, Schick et al. manuscript on entanglement

#' Create valid and usable variables describing the start/stop dates of entanglement windows
#' 
#' The primary goal of this is to clean up the entanglement data a bit. We do this by
#' adding in information in the comments about each event, and coding that into a new
#' variable. We also extract the sex from the comments, and the age of the animal.
#' 
#' @return \code{tangled} a data frame containing the cleaned entanglement data
#' @export
makeTangle <- function() {
  library(stringr)
  library(lubridate)
  
  tangled$StartDate <- ymd(tangled$StartDate)
  tangled$EndDate <- ymd(tangled$EndDate)
  
  idx <- which(tangled$StartDate <= ymd("1900-01-02"))
  tangled[idx, c("StartDate")] <- NA  # I'm doing this because these are fictitious, i.e. there is no real known start date. So I want to zero out anything that was based on those start dates.
  
  
  comments <- str_split(tangled$EntanglementComment, ";")
  
  tangled$AgeSex <- rep(NA, nrow(tangled))
  tangled$TimeFrame <- rep(NA, nrow(tangled))
  tangled$Severity <- rep(NA, nrow(tangled))
  
  # Most of these are from entanglement scars, but there are
  # cases that have gear. The next bit is to find them and mark
  # those with a 1 (0 otherwise)
  gear.idx <- which(!is.na(str_match(tangled$EntanglementComment, 
    "GEAR")))
  tangled$gear <- rep(0, nrow(tangled))
  tangled[gear.idx, "gear"] <- 1
  
  minor.idx <- which(!is.na(str_match(tangled$EntanglementComment, 
    "MINOR")))
  tangled[minor.idx, "Severity"] <- "minor"
  
  moderate.idx <- which(!is.na(str_match(tangled$EntanglementComment, 
    "MODERATE")))
  tangled[moderate.idx, "Severity"] <- "moderate"
  
  severe.idx <- which(!is.na(str_match(tangled$EntanglementComment, 
    "SEVERE")))
  tangled[severe.idx, "Severity"] <- "severe"
  
  dead.idx <- which(!is.na(str_match(tangled$EntanglementComment, 
    "DEAD")))
  tangled$LiveStatus <- rep("ALIVE", nrow(tangled))
  tangled[dead.idx, "LiveStatus"] <- "DEAD"
  
  
  for (i in 1:nrow(tangled)) {
    tangled$AgeSex[i] <- comments[[i]][1]
    tangled$TimeFrame[i] <- comments[[i]][2]
  }
  
  agesex <- str_split(tangled$AgeSex, " female")
  males <- str_trim(str_match(tangled$AgeSex, " male"))
  females <- str_trim(str_match(tangled$AgeSex, " female"))
  
  fdx <- which(females == "female", arr.ind = T)
  tangled$Gender <- rep(NA, nrow(tangled))
  tangled[fdx, "Gender"] <- females[fdx]
  
  mdx <- which(males == "male", arr.ind = T)
  tangled[mdx, "Gender"] <- males[mdx]
  return(tangled)
}