data-raw/R/create_real_fishery_lencomp.R

In NOAA-EDAB/ms-keyrun: All information for keyrun review

#' Length abundance and biomass by length
#'
#'Read and format output from mscatch to mskeyrun
#'
#'same format as: mskeyrun::mskeyrun::simFisheryLencomp
#'
#'
#'
#'
library(magrittr)

create_real_fishery_lencomp <- function(convertKGtoMT=T,outPath=NULL) {
  
  # 1kg = 2.2046226218 lbs
  
  
  if (convertKGtoMT  == T) {
    scalar <- 1000
    unitsLabel <- "metric tons"
  } else {
    scalar <- 1
    unitsLabel <- "kilograms"
  }
  
  
  itis <- mscatch::speciesLookupTable %>%
    dplyr::distinct(SPECIES_ITIS) %>%
    dplyr::filter(!(SPECIES_ITIS %in% c(164727,166774))) %>%
    dplyr::pull()
  
  realFisheryLencomp <- NULL
  
  for (it in itis) {
    # expandedLandings in kgs. This is referencing mscatch dir structure
    fileNmLen <- here::here("data-raw/data/",paste0("expandedLandings",it,".rds"))
    
    message(paste0("Reading itis = ",it))
    speciesDataLen <- readRDS(fileNmLen)
    
    name <- mscatch::speciesLookupTable %>%
      dplyr::filter(SPECIES_ITIS == it) %>%
      dplyr::pull(COMMON_NAME.y) %>%
      unique() %>%
      abutils::capitalize_first_letter()
    ## process data
    #ModSim        year Code  Name         fishery lenbin variable value units
    
    speciesFormat <- speciesDataLen %>%
      dplyr::group_by(YEAR,NEGEAR,LENGTH,species_itis) %>%
      dplyr::summarise(biomass = sum(weight)/scalar,
                       abundance = sum(numbers),
                       .groups="drop") %>%
      dplyr::rename(year=YEAR,Code=species_itis,fishery=NEGEAR,lenbin = LENGTH) %>%
      dplyr::mutate(Name = name,
                    ModSim = "Actual") %>%
      tidyr::pivot_longer(.,cols=c(biomass,abundance),
                          names_to = "variable",
                          values_to = "value") %>%
      dplyr::mutate(units = dplyr::case_when(variable == "biomass" ~ unitsLabel,
                                             variable == "abundance" ~ "numbers")) %>%
      dplyr::select(ModSim,year,Code,Name,fishery,lenbin,variable,value,units)
    
    
    realFisheryLencomp <- rbind(realFisheryLencomp,speciesFormat)
    
    
  }
  
  realFisheryLencomp <- realFisheryLencomp %>%
    dplyr::mutate(Code = as.double(Code))
  
  if (!is.null(outPath)) {
    save(realFisheryLencomp,file=outPath)
  }
  
  
  return(realFisheryLencomp)
}