R/describe_text.R

In nwfsc-math-bio/VRData: NWFSC PNW Salmonid Viability Reports Data Package

#' describe_text
#'
#' Adds the format code for the Roxygen data header by reading in the 
#' columns names and only adding the needed items.
#' 
#' @param thecols the column names from the file
#' @keywords internal
describe_text <- function(thecols, compiler=""){
  key <- matrix(c(
    "NMFS_POPID", "NWFSC id for the population.",
    "POPID", "NWFSC id for the population.",
    "POP_ID", "NWFSC id for the population.",
    "ESU", "ESU or DPS name.",
    "DPS", "ESU or DPS name.",
    "MAJOR_POPULATION_GROUP", "Major population group within the ESU or DPS.",
    "MPG", "Major population group within the ESU or DPS.",
    "POPULATION_NAME", "Long population name.",
    "COMMON_POPULATION_NAME", "Shorter population name used in Viability Report figures and tables.",
    "SPECIES", "Species name.",
    "RUN_TIMING", "Run timing (fall, winter, spring, etc). If missing, see the ESU/DPS name or may not be applicable for the species.",
    "YEAR", "Integer in XXXX format. The year that the count was made. See details for ESU or DPS specific comments.",
    "BROOD_YEAR", "Integer in XXXX format. The year that the count was made. See details for ESU or DPS specific comments.",
    "NUMBER_OF_SPAWNERS", "Total spawners or escapement count. -99 means missing count. May be integer or decimal.",
    "FRACWILD", "Decimal between 0 and 1. Fraction wild or natural. -99 means missing information.",
    "FRACTION_WILD", "Decimal between 0 and 1. Fraction wild or natural. -99 means missing information.",
    "CITATION", "Data citation. Listed under References below.",
    "SOURCE", "Data contributor.  Listed under Source below.",
    "METHOD", "Method for the spawner count. Survey refers to a spawning ground survey; the count itself is an expansion. See the SPS (database link in sources below) for the details for the data. LadderCount is a weir or dam count. Model  refers to the DABOM model that expands from PIT tag data. GSI is an expansion based on the BOXCAR model, which uses GSI to allocate fish sampled at Lower Granite Dam.",
    "CONTRIBUTOR", "Data contributor. Listed under Source below.",
    "COMPILER", paste("NWFSC staff who compiled the data file:", compiler),
    "SERIES", "For certain populations, there are multiple types of spawner count data. For example survey and model counts that are based on different methods. In this case, the 'Series' column gives a name for the dataset to distinguish it from other data sets of the same population."
  ),ncol=2, byrow = TRUE)
  
  thetext <- c("#' \n#' @format A csv file.\n#' \\describe{")
  
  for(i in thecols){
    loc <- match(stringr::str_to_lower(i), stringr::str_to_lower(key[,1]))
    if(is.na(loc)) next
    thetext <- c(thetext, paste0("#' \\item{", i, "}{", key[loc,2], "}"))
  }
  thetext <- c(thetext, "#' }\n#' ")
  
  return(thetext) 
}