R/crop_to_strata.R

In NOAA-EDAB/ECSA: Ecosystem Context for Stock Advice

#' 
#'
#'
#'
#'
#'


loadRData <- function(fileName){
  load(fileName)
  get(ls()[ls() != "fileName"])
}

#'
#'
#'@param r 
#'@param stock_name
#'@param stock_season
#'@param common_name
#'@param season_
#'@param mask_type
#'
#'@return 
#'
#'
#'@importFrom magrittr "%>%"
#'

crop_to_strata <- function(r, stock_name, stock_season, common_name, season_, mask_type = "unit"){
  
  `%>%` <- magrittr::`%>%`
  
  s1 <- read.csv(here::here('data','stock_data','stock_list.csv'),
                 stringsAsFactors = F) %>% 
    dplyr::filter(stringr::str_detect(stock_name, !!stock_name)) 
  
  if (nrow(s1) == 0) stop("No strata in query. Check common name spelling.")
  
  strata <- s1 %>% 
    dplyr::filter(stock_season %in% stock_season) %>% 
    dplyr::select(strata, stock_season)
  
  if (nrow(strata) == 0) {
    stop(paste("No strata in query. Available stock area selections include:",unique(s1$stock_season)))
  }
  
  # Load strata
  strata <- map_strata(stock_name = stock_name,
                       stock_season = stock_season,
                       common_name = common_name,
                       strata = strata,
                       save_plot = F,
                       get_sf = T) %>%  
    methods::as("sf") %>% 
    sf::st_transform(st_crs("+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0")) %>% 
    dplyr::select_at(.,vars(geometry, stock_season))
  
  
  # Load raster and convert to stars
  r <- loadRData(here::here("data-raw",r)) 
  raster::crs(r) <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
  r <- stars::st_as_stars(r)
  
  # Crop input raster to match strata
  out <- r[strata]
  
  return(out)

}