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nsink_get_data.R
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nsink_get_data.R
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#' Gets N-Sink data for a given HUC
#'
#' The required datasets for the N-sink analysis are available from multiple,
#' online resources. This function takes a HUC as input and downloads local
#' copies of those datasets. It will place these in a local directory and
#' inside that directory a new folder for each NHD Plus raster processing unit
#' will be created. If you use the same folder for the data directory, it will
#' act as a cache (imperfect, though) and only download any new datasets that
#' have not already been downloaded.
#' @param huc A character string of a HUC identifier. Currently can run only
#' a single HUC at a time. This package was developed using 12-digit
#' HUCS, but has been (lightly) tested with larger HUCs and appears
#' to work, but is not certain for all cases.
#' @param data_dir A directory to store N-Sink data downloads. Defaults to
#' "nsink_data" inside of the current working directory.
#' Created if it doesn't exist. May be used for multiple HUCs
#' and only data that doesn't currently exist will be
#' downloaded.
#' @param force Logical to determine if files should be downloaded
#' again if they already exist locally.
#' @param year An argument to be passed to FedData's \code{\link{get_nlcd}}
#' function. Default is 2016.
#' @export
#' @importFrom methods as
#' @return Returns a list with the huc used and the directory where the data is
#' stored.
#' @examples
#' \dontrun{
#' library(nsink)
#' niantic_huc <- nsink_get_huc_id("Niantic River")$huc_12
#' nsink_get_data(huc = niantic_huc, data_dir = "nsink_data", force = TRUE)
#' }
nsink_get_data <- function(huc, data_dir = normalizePath("nsink_data",
winslash = "/",
mustWork = FALSE),
force = FALSE, year = "2016") {
year <- as.character(year)
huc <- as.character(huc)
if (nchar(gsub("[[:alpha:]]+", "", huc)) %% 2 != 0) {
stop("The supplied huc does not appear to have an even number of digits. If HUC has a leading 0, pass as character")
}
# Get rpu
rpu <- unique(wbd_lookup[grepl(paste0("^", huc), wbd_lookup$HUC_12),]$RPU)
rpu <- rpu[!is.na(rpu)]
data_dir_orig <- data_dir
for(i in seq_along(rpu)){
#Add RPU to data_dir
data_dir <- data_dir_orig
while(grepl(rpu[i], basename(data_dir))){
data_dir <- dirname(data_dir)
message("Do not include the RPU in the data directory.")
}
data_dir <- paste(data_dir, rpu[i], sep = "/")
# Check for/create/clean data directory
data_dir <- nsink_fix_data_directory(data_dir)
# urls
attr_url <- nsink_get_plus_remotepath(rpu[i], "NHDPlusAttributes")
erom_url <- nsink_get_plus_remotepath(rpu[i], "EROMExtension")
nhd_url <- nsink_get_plus_remotepath(rpu[i], "NHDSnapshot")
fdr_url <- nsink_get_plus_remotepath(rpu[i], "FdrFac")
wbd_url <- nsink_get_plus_remotepath(rpu[i], "WBDSnapshot")
# get nhdplus data
message("Getting NHDPlus files...")
attr <- get_nhd_plus(attr_url, data_dir, force)
erom <- get_nhd_plus(erom_url, data_dir, force)
nhd <- get_nhd_plus(nhd_url, data_dir, force)
fdr <- get_nhd_plus(fdr_url, data_dir, force)
wbd <- get_nhd_plus(wbd_url, data_dir, force)
# unzip nhdplus data
message("Unzipping NHDPlus files ...")
if(!dir.exists(paste0(data_dir, "attr"))){
attr_z <- archive::archive_extract(paste0(data_dir, basename(attr_url)),
paste0(data_dir, "attr"))
}
if(!dir.exists(paste0(data_dir, "erom"))){
erom_z <- archive::archive_extract(paste0(data_dir, basename(erom_url)),
paste0(data_dir, "erom"))
}
if(!dir.exists(paste0(data_dir, "nhd"))){
nhd_z <- archive::archive_extract(paste0(data_dir, basename(nhd_url)),
paste0(data_dir, "nhd"))
}
if(!dir.exists(paste0(data_dir, "fdr"))){
fdr_z <- archive::archive_extract(paste0(data_dir, basename(fdr_url)),
paste0(data_dir, "fdr"))
}
if(!dir.exists(paste0(data_dir, "wbd"))){
wbd_z <- archive::archive_extract(paste0(data_dir, basename(wbd_url)),
paste0(data_dir, "wbd"))
}
# Use actual huc to limit downloads on impervious and ssurgo
huc_sf_file <- list.files(paste0(data_dir, "wbd"), "WBD_Subwatershed.shp", full.names = TRUE,
recursive = TRUE)
huc_sf <- sf::st_read(huc_sf_file,quiet = TRUE)
huc_12 <- huc_sf[grepl(paste0("^", huc), huc_sf$HUC_12), ]
huc_12 <- mutate(huc_12, selected_huc = huc)
huc_12 <- group_by(huc_12, .data$selected_huc)
huc_12 <- summarize(huc_12, selected_huc = unique(.data$selected_huc))
huc_12 <- ungroup(huc_12)
# Get impervious
mrlc <- httr::GET("https://www.mrlc.gov")
if(mrlc$status_code != 200){
warning("The MRLC site does not appear to be available and the impervious surface and NLCD are not downloaded. Try again later.")
} else if(mrlc$status_code == 200){
message("Getting Impervious Surface ...")
imp <- FedData::get_nlcd(
template = huc_12, dataset = "impervious",
label = huc, extraction.dir = paste0(data_dir, "imperv"),
force.redo = force, year = year)
# Get 2011 NLCD
message("Getting NLCD ...")
nlcd <- FedData::get_nlcd(
template = huc_12, dataset = "landcover",
label = huc, extraction.dir = paste0(data_dir, "nlcd"),
force.redo = force, year = year)
}
# Get SSURGO
# This would occasional have connection reset and FedData would throw
# an error. Connection would eventually work. This code repeats it until it
# works or it tries it 10 times. THis is an ugly hack but works and doesn't
# end in an infinite loop.
# FedData::get_ssurgo will throw parsing warnings if data already downloaded.
sdm <- httr::GET("https://sdmdataaccess.sc.egov.usda.gov")
wss <- httr::GET("https://websoilsurvey.sc.egov.usda.gov/App/HomePage.htm")
if(sdm$status_code != 200 | wss$status_code != 200){
warning("The required SSURGO sites do not appear to be available and the SSURGO data are not downloaded. Try again later.")
} else if(sdm$status_code == 200 & wss$status_code == 200){
message("Getting SSURGO...")
repeat_it <- TRUE
count <- 0
while(is.logical(repeat_it) & count <= 9) {
count <- count + 1
repeat_it <- tryCatch(
suppressMessages({
suppressWarnings({
ssurgo <- FedData::get_ssurgo(huc_12,
label = huc,
extraction.dir = paste0(data_dir, "ssurgo"),
raw.dir = paste0(data_dir, "ssurgo"),
force.redo = force)
})
})
,
error = function(e) TRUE
)
}
}
if(is.logical(repeat_it) & count > 9){
ssurgo <- FedData::get_ssurgo(huc_12,
label = huc,
extraction.dir = paste0(data_dir, "ssurgo"),
raw.dir = paste0(data_dir, "ssurgo"),
force.redo = force)
stop("SSURGO did not download correctly. Try again or check package FedData
for possible clues as to why FedData::get_ssurgo is not able to
download the soils data.")
}
}
# Return a list with the huc and the data_dir
list(huc = huc, data_dir = data_dir_orig)
}
#' Look up HUC 12 ID from a HUC name
#'
#' This function takes a HUC Name and returns matching HUC 12 IDs. The default
#' behavior is to select all possible matching IDs without matching the case of
#' the string. If an exact match is required, use the \code{exact} argument.
#'
#' @param huc_name Character string of a HUC Name or partial HUC name
#' @param exact Logical indicating whether or not to do an exact match
#' @return A data frame with HUC_12 and HU_12_NAME that match the huc_name
#' @importFrom dplyr tibble
#' @export
#' @examples
#' nsink_get_huc_id(huc_name = "Niantic River")
nsink_get_huc_id <- function(huc_name, exact = FALSE) {
if (exact) {
idx <- wbd_lookup$HU_12_NAME == huc_name
} else {
idx <- grepl(tolower(huc_name), tolower(wbd_lookup$HU_12_NAME))
}
idx[is.na(idx)]<-FALSE
wbd_match <- wbd_lookup[idx, ]
tibble(
huc_12 = wbd_match$HUC_12, huc_12_name = wbd_match$HU_12_NAME,
state = wbd_match$STATES
)
}