R/ReadInLengths.R

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

#' Reads in the compositional survey data and filters the data into what is necessary
#' It reads in catch and station data and makes sure only the species necessary are kept
#' ### may want to keep NA (blank in Excel) to select the zero tows
#' removeCAN is a flag if you want tows in Canadian waters removed
#'    need the file called foreign_hauls.csv
#'
#' Necessary column names
#'    SPECIES_CODE
#'    LENGTH
#'
#' @param dat data file name
#' @template verbose
#'
#' @author Allan Hicks and Chantel Wetzel
#' @export

ReadInLengths.fn <- function(dat, verbose = TRUE) {
  totRows <- nrow(dat)
  dat <- dat[!is.na(dat$Length_cm), ]
  dat$Weight <- as.numeric(as.character(dat$Weight_kg))
  dat$year <- as.numeric(as.character(dat$Year))
  dat$Depth_m <- as.numeric(as.character(dat$Depth_m))
  dat$Length_cm <- as.numeric(as.character(dat$Length_cm))
  dat$Age <- as.numeric(as.character(dat$Age))


  if (verbose) {
    cat("There are ", nrow(dat), " of length kept out of", totRows, "after removing missing lengths\n")
  }


  return(dat)
}