fix #219 change seaice fxn to sea_ice, painful to change fxn name

but wanted to change user interface, so useful i think to change fxn name to make it easier
updated tests

DESCRIPTION

@@ -54,6 +54,7 @@ Suggests:
     raster,
     leaflet,
     rgdal,
+    sf,
     rmarkdown,
     purrr,
     ggmap,

NAMESPACE

@@ -102,6 +102,7 @@ export(noaa_stations)
 export(readshpfile)
 export(se_data)
 export(se_files)
+export(sea_ice)
 export(seaice)
 export(seaice_tabular)
 export(seaiceeurls)

R/defunct.R

@@ -167,6 +167,14 @@ ncdc_leg_data <- function() {
   .Defunct(msg = "This function is defunct, see ncdc_*() functions")
 }
 
+#' This function is defunct.
+#' @export
+#' @rdname seaice-defunct
+#' @keywords internal
+seaice <- function() {
+  .Defunct(msg = "This function is defunct, see sea_ice()")
+}
+
 #' Defunct functions in rnoaa
 #'
 #' \itemize{
@@ -196,6 +204,7 @@ ncdc_leg_data <- function() {
 #'  \item \code{\link{ncdc_leg_sites}}: Removed. See \code{NCDC Legacy} below
 #'  \item \code{\link{ncdc_leg_site_info}}: Removed. See \code{NCDC Legacy} below
 #'  \item \code{\link{ncdc_leg_data}}: Removed. See \code{NCDC Legacy} below
+#'  \item \code{\link{seaice}}: Replaced with \code{\link{sea_ice}}
 #' }
 #' 
 #' @section NCDC Legacy:

R/seaice.r

@@ -1,32 +1,56 @@
 #' Get sea ice data.
 #'
 #' @export
-#' @param url A url for a NOAA sea ice ftp file
-#' @param ... Further arguments passed on to readshpfile function, see
-#' `readshpfile`
-#' @return A data.frame
-#' @details If you want to reproject the shape files, use
+#' @param year (numeric) a year
+#' @param month (character) a month, as character abbrevation of a month
+#' @param pole (character) one of S (south) or N (north)
+#' @param format (character) one of shp (default), geotiff-extent (for geotiff
+#' extent data), or geotiff-conc (for geotiff concentration data)
+#' @param ... Further arguments passed on to `rgdal::readshpfile()` if
+#' `format="shp"` or `raster::raster()` if not
+#' @return data.frame if `format="shp"`; `raster::raster()` if not
+#' @details For shp files, if you want to reproject the shape files, use
 #' [readshpfile()] to read in shape file, then reproject, and so on.
 #' @seealso [seaice_tabular()]
+#' @references See the "User Guide" pdf at https://nsidc.org/data/g02135
 #' @examples \dontrun{
-#' # Look at data.frame's for a series of years for Feb, South pole
-#' urls <- sapply(seq(1979,1990,1), function(x) seaiceeurls(yr=x,
-#'   mo='Feb', pole='S'))
-#' out <- lapply(urls, seaice)
-#' lapply(out, head)
+#' # the new way
+#' library(raster)
+#' library(sf)
+#'
+#' ## one file
+#' sea_ice(year = 1990, month = "Apr", pole = "N")
+#' sea_ice(year = 1990, month = "Apr", pole = "N", format = "geotiff-extent")
+#' sea_ice(year = 1990, month = "Apr", pole = "N", format = "geotiff-conc")
+#' ## many files
+#' sea_ice(year = 1990, month = "Apr")
+#' x <- sea_ice(year = 1990, month = "Apr", format = "geotiff-extent")
+#' y <- sea_ice(year = 1990, month = "Apr", format = "geotiff-conc")
+#' plot(x[[1]])
+#' plot(y[[1]])
 #'
 #' # Map a single year/month/pole combo
-#' urls <- seaiceeurls(mo='Apr', pole='N', yr=1990)
-#' out <- seaice(urls)
-#' library('ggplot2')
-#' ggplot(out, aes(long, lat, group=group)) +
-#'    geom_polygon(fill="steelblue") +
-#'    theme_ice()
+#' out <- sea_ice(year = 1990, month = 'Apr', pole = 'N')
+#' library('sf')
+#' plot(out[[1]])
 #' }
-seaice <- function(url, ...) {
-  check4pkg("rgdal")
-  tt <- readshpfile(url, ...)
-  suppressMessages(fortify(tt))
+sea_ice <- function(year = NULL, month = NULL, pole = NULL, format = "shp",
+  ...) {
+
+  assert(year, c('integer', 'numeric'))
+  assert(month, 'character')
+  assert(pole, 'character')
+  assert(format, 'character')
+  if (!format %in% c("shp", "geotiff-extent", "geotiff-conc"))
+    stop("'format' must be one of: 'shp', 'geotiff-extent', 'geotiff-conc'")
+  urls <- seaiceeurls(yr=year, mo=month, pole, format)
+  if (format == "shp") {
+    check4pkg("sf")
+    lapply(urls, readshpfile, ...)
+  } else {
+    check4pkg("raster")
+    lapply(urls, raster::raster, ...)
+  }
 }
 
 #' Make all urls for sea ice data
@@ -49,14 +73,47 @@ seaice <- function(url, ...) {
 #'
 #' # Get urls for Feb of 1980, just S pole
 #' seaiceeurls(yr=1980, mo='Feb', pole='S')
+#'
+#' # GeoTIFF
+#' seaiceeurls(yr=1980, mo='Feb', pole='S', format = "geotiff")
 #' }
-seaiceeurls <- function(yr = NULL, mo = NULL, pole = NULL) {
-  # previous years
+seaiceeurls <- function(yr = NULL, mo = NULL, pole = NULL, format = "shp") {
+  type <- if (!grepl("geotiff", format)) NULL else strsplit(format, "-")[[1]][2]
+  urls <- generate_urls(format, type)
+  if (!is.null(pole)) {
+    pole <- switch(format, shp=sprintf("_%s_", pole), sprintf("%s_", pole))
+  }
+  if (!is.null(yr)) yr <- sprintf("_%s", yr)
+
+  ss <- urls
+  if (!is.null(yr) & is.null(mo) & is.null(pole))
+    ss <- grep(yr, urls, value = TRUE)
+  if (is.null(yr) & !is.null(mo) & is.null(pole))
+    ss <- grep(mo, urls, value = TRUE)
+  if (is.null(yr) & is.null(mo) & !is.null(pole))
+    ss <- grep(pole, urls, value = TRUE)
+  if (!is.null(yr) & !is.null(mo) & is.null(pole))
+    ss <- grep(yr, grep(mo, urls, value = TRUE), value = TRUE)
+  if (!is.null(yr) & is.null(mo) & !is.null(pole))
+    ss <- grep(yr, grep(pole, urls, value = TRUE), value = TRUE)
+  if (is.null(yr) & !is.null(mo) & !is.null(pole))
+    ss <- grep(pole, grep(mo, urls, value = TRUE), value = TRUE)
+  if (!is.null(yr) & !is.null(mo) & !is.null(pole))
+    ss <- grep(yr, grep(pole, grep(mo, urls, value = TRUE),
+                        value = TRUE), value = TRUE)
+
+  return( ss )
+}
+
+generate_urls <- function(format, type) {
+  fun <- if (format == "shp") make_urls_shp else make_urls_geotiff
+  if (!is.null(type)) type <- switch(type, extent = "extent", "concentration")
+
   yrs_prev <- seq(1979, year(today()) - 1, 1)
   months_prevyr <- c(paste0(0, seq(1, 9)), c(10, 11, 12))
   yrs_months <- do.call(c, lapply(yrs_prev, function(x)
     paste(x, months_prevyr, sep = '')))
-  urls <- make_seaice_urls(yrs_months, month.abb)
+  urls <- fun(yrs_months, month.abb, type = type)
 
   # this year
   months_thisyr <- seq(1, as.numeric(format(Sys.Date(), "%m")))
@@ -68,38 +125,16 @@ seaiceeurls <- function(yr = NULL, mo = NULL, pole = NULL) {
     yrs_months_thisyr <- paste0(format(Sys.Date(), "%Y"), months_thisyr)
     eachmonth_thiyr <- month.abb[1:grep(format(Sys.Date() - months(1), "%b"),
                                         month.abb)]
-    urls_thisyr <- make_seaice_urls(yrs_months_thisyr, eachmonth_thiyr)
+    urls_thisyr <- fun(yrs_months_thisyr, eachmonth_thiyr, type = type)
   } else {
     urls_thisyr <- c()
   }
 
   # all urls
-  allurls <- c(urls, urls_thisyr)
-
-  if (!is.null(pole)) pole <- sprintf("_%s_", pole)
-  if (!is.null(yr)) yr <- sprintf("_%s", yr)
-
-  ss <- allurls
-  if (!is.null(yr) & is.null(mo) & is.null(pole))
-    ss <- grep(yr, allurls, value = TRUE)
-  if (is.null(yr) & !is.null(mo) & is.null(pole))
-    ss <- grep(mo, allurls, value = TRUE)
-  if (is.null(yr) & is.null(mo) & !is.null(pole))
-    ss <- grep(pole, allurls, value = TRUE)
-  if (!is.null(yr) & !is.null(mo) & is.null(pole))
-    ss <- grep(yr, grep(mo, allurls, value = TRUE), value = TRUE)
-  if (!is.null(yr) & is.null(mo) & !is.null(pole))
-    ss <- grep(yr, grep(pole, allurls, value = TRUE), value = TRUE)
-  if (is.null(yr) & !is.null(mo) & !is.null(pole))
-    ss <- grep(pole, grep(mo, allurls, value = TRUE), value = TRUE)
-  if (!is.null(yr) & !is.null(mo) & !is.null(pole))
-    ss <- grep(yr, grep(pole, grep(mo, allurls, value = TRUE),
-                        value = TRUE), value = TRUE)
-
-  return( ss )
+  c(urls, urls_thisyr)
 }
 
-make_seaice_urls <- function(yrs_months, mos) {
+make_urls_shp <- function(yrs_months, mos, type = NULL) {
   do.call(
     "c",
     lapply(c('south', 'north'), function(x) {
@@ -110,17 +145,38 @@ make_seaice_urls <- function(yrs_months, mos) {
         mos,
         sep = "_"
       )
-      tmp <- sprintf(seaiceftp, x, mm)
+      tmp <- sprintf(ftp_url_shp, x, mm)
       route <- paste('extent_', switch(x, south = "S", north = "N"),
                      '_', yrs_months, '_polygon_v3.0.zip',
                      sep = '')
       file.path(tmp, route)
     })
   )
 }
+make_urls_geotiff <- function(yrs_months, mos, type = "extent") {
+  do.call(
+    "c",
+    lapply(c('south', 'north'), function(x) {
+      mm <- paste(
+        vapply(seq_along(mos), function(z) {
+          if (nchar(z) == 1) paste0(0, z) else as.character(z)
+        }, ""),
+        mos,
+        sep = "_"
+      )
+      tmp <- sprintf(ftp_url_geotiff, x, mm)
+      route <- paste(switch(x, south = "S", north = "N"),
+                     '_', yrs_months, sprintf('_%s_v3.0.tif', type),
+                     sep = '')
+      file.path(tmp, route)
+    })
+  )
+}
 
-seaiceftp <-
+ftp_url_shp <-
   'ftp://sidads.colorado.edu/DATASETS/NOAA/G02135/%s/monthly/shapefiles/shp_extent/%s'
+ftp_url_geotiff <-
+  'ftp://sidads.colorado.edu/DATASETS/NOAA/G02135/%s/monthly/geotiff/%s'
 
 #' Function to read shapefiles
 #'
@@ -144,7 +200,8 @@ readshpfile <- function(x, storepath = NULL) {
   dir.create(path_write, showWarnings = FALSE)
   unzip(path, exdir = path_write)
   my_layer <- rgdal::ogrListLayers(path.expand(path_write))
-  rgdal::readOGR(path.expand(path_write), layer = my_layer, verbose = FALSE)
+  sf::st_as_sf(rgdal::readOGR(path.expand(path_write), layer = my_layer,
+    verbose = FALSE, stringsAsFactors = FALSE))
 }
 
 #' ggplot2 map theme

R/seaice_tabular.R

@@ -2,19 +2,25 @@ si_tab_pat <- "ftp://sidads.colorado.edu/DATASETS/NOAA/G02135/%s/monthly/data/"
 
 #' Sea ice tabular data
 #'
+#' Collects `.csv` files from NOAA, and binds them together into
+#' a single data.frame. Data across years, with extent and area of ice.
+#' 
+#' An example file, for January, North pole:
+#' `ftp://sidads.colorado.edu/DATASETS/NOAA/G02135/north/monthly/data/N_01_extent_v3.0.csv`
+#'
 #' @export
 #' @param ... Curl options passed on to [crul::verb-GET] - beware
 #' that curl options are passed to each http request, for each of
 #' 24 requests.
 #' @return A data.frame with columns:
-#' 
+#'
 #' - year (integer)
 #' - mo (integer)
 #' - data.type (character)
 #' - region (character)
 #' - extent (numeric)
 #' - area (numeric)
-#' 
+#'
 #' @details a value in any cell of -9999 indicates missing data
 #' @seealso [seaice()]
 #' @examples \dontrun{