#30 started work on ecoregions

DESCRIPTION

@@ -28,7 +28,9 @@ Imports:
     lazyeval,
     crul,
     jsonlite,
-    tibble
+    tibble,
+    hoardr,
+    curl
 Suggests:
     testthat,
     knitr,

R/ecoregion.R

@@ -0,0 +1,108 @@
+#' Filter points within ecoregions
+#'
+#' @export
+#' @param x (data.frame) A data.frame
+#' @param dataset (character) the dataset to use. one of: "meow" (Marine
+#' Ecoregions of the World), "fao" (). See Details.
+#' @param ecoregion (character) the ecoregion name. See Details.
+#' @param lat,lon (character) Latitude and longitude column to use. See Details.
+#' @param drop (logical) Drop bad data points or not. Either way, we parse out
+#' bad data points as an attribute you can access. Default: `TRUE`
+#' @param ignore.na (logical) To consider NA values as a bad point or not.
+#' Default: `FALSE`
+#' @return Returns a data.frame, with attributes
+#' @details see `scrubr_cache` for managing the cache of data
+#' @section Datasets: and ecoregions:
+#'
+#' - meow: https://opendata.arcgis.com/datasets/ed2be4cf8b7a451f84fd093c2e7660e3_0.geojson
+#' - fao:http://www.fao.org/geonetwork/srv/en/main.home?uuid=ac02a460-da52-11dc-9d70-0017f293bd28
+#' http://www.fao.org/figis/geoserver/area/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=area:FAO_AREAS&outputFormat=SHAPE-ZIP
+#' http://www.fao.org/figis/geoserver/area/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=area:FAO_AREAS&outputFormat=application/json
+#'
+#' @section Ecoregions:
+#'
+#' - meow: 
+#' - fao: asdfasdf
+#'
+#' @examples
+#' ## Marine Ecoregions of the World
+#' wkt <- 'POLYGON((-119.8 12.2, -105.1 11.5, -106.1 21.6, -119.8 20.9, -119.8 12.2))'
+#' res <- rgbif::occ_data(geometry = wkt, limit=300)$data
+#' res2 <- sf::st_as_sf(res, coords = c("decimalLongitude", "decimalLatitude"))
+#' res2 <- sf::st_set_crs(res2, 4326)
+#' mapview::mapview(res2)
+#' tmp <- ecoregion(dframe(res), dataset = "meow",
+#'    ecoregion = "ECOREGION:Mexican Tropical Pacific")
+#' tmp2 <- sf::st_as_sf(tmp, coords = c("decimalLongitude", "decimalLatitude"))
+#' tmp2 <- sf::st_set_crs(tmp2, 4326)
+#' mapview::mapview(tmp2)
+#' 
+#' ## FAO
+#' wkt <- 'POLYGON((72.2 38.5,-173.6 38.5,-173.6 -41.5,72.2 -41.5,72.2 38.5))'
+#' manta_ray <- rgbif::name_backbone("Mobula alfredi")$usageKey
+#' res <- rgbif::occ_data(manta_ray, geometry = wkt, limit=300, hasCoordinate = TRUE)
+#' dat <- sf::st_as_sf(res$data, coords = c("decimalLongitude", "decimalLatitude"))
+#' dat <- sf::st_set_crs(dat, 4326)
+#' mapview::mapview(dat)
+#' tmp <- ecoregion(dframe(res$data), dataset = "fao", ecoregion = "OCEAN:Indian")
+#' library(dplyr)
+#' tmp <- filter(tmp, !is.na(decimalLongitude))
+#' tmp2 <- sf::st_as_sf(tmp, coords = c("decimalLongitude", "decimalLatitude"))
+#' tmp2 <- sf::st_set_crs(tmp2, 4326)
+#' mapview::mapview(tmp2)
+ecoregion <- function(x, dataset = "meow", ecoregion,
+  lat = NULL, lon = NULL, drop = TRUE) {
+
+  check4pkg("sf")
+  assert(dataset, "character")
+  stopifnot(dataset %in% c("meow", "fao"))
+  assert(ecoregion, "character")
+  stopifnot(grepl(":", ecoregion))
+  scrubr_cache$mkdir()
+
+  x <- do_coords(x, lat, lon)
+  z <- sf::st_as_sf(x, coords = c("longitude", "latitude"))
+  z <- sf::st_set_crs(z, 4326)
+
+  ref_sf <- switch(dataset, meow = do_meow(), fao = do_fao())
+  er_split <- strsplit(ecoregion, ":")[[1]]
+  ref_target <- ref_sf[ref_sf[[er_split[1]]] %in% er_split[2], ]
+
+  bb <- sf::st_join(z, ref_target, join = sf::st_within)
+  wth <- tibble::as_tibble(x[is.na(bb$FID), ])
+
+  if (drop) {
+    x <- tibble::as_tibble(x[!is.na(bb$FID), ])
+  }
+  if (NROW(wth) == 0) wth <- NA
+  row.names(wth) <- NULL
+  row.names(x) <- NULL
+  structure(reassign(x), coord_ecoregion = wth,
+    dataset = dataset, ecoregion = ecoregion)
+}
+
+do_meow <- function() {
+  path <- file.path(scrubr_cache$cache_path_get(), "meow.geojson")
+  if (file.exists(path)) {
+    message("meow.geojson exists in the cache")
+  } else {
+    meow_url <- "https://opendata.arcgis.com/datasets/ed2be4cf8b7a451f84fd093c2e7660e3_0.geojson"
+    curl::curl_download(meow_url, path)
+  }
+  sf::read_sf(path)
+}
+# w <- do_meow()
+# mapview::mapview(w)
+
+do_fao <- function() {
+  path <- file.path(scrubr_cache$cache_path_get(), "fao.geojson")
+  if (file.exists(path)) {
+    message("fao.geojson exists in the cache")
+  } else {
+    fao_url <- "http://www.fao.org/figis/geoserver/area/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=area:FAO_AREAS&outputFormat=application/json"
+    curl::curl_download(fao_url, path)
+  }
+  sf::read_sf(path)
+}
+# z <- do_fao()
+# mapview::mapview(z)

R/onload.R

@@ -0,0 +1,7 @@
+scrubr_cache <- NULL
+
+.onLoad <- function(libname, pkgname){
+  x <- hoardr::hoard()
+  x$cache_path_set("scrubr")
+  scrubr_cache <<- x
+}

R/scrubr-package.R

@@ -10,6 +10,8 @@
 #' @importFrom Matrix as.matrix
 #' @importFrom magrittr %>%
 #' @importFrom methods as
+#' @importFrom hoardr hoard
+#' @importFrom curl curl_download
 #' @name scrubr-package
 #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com}
 #' @aliases scrubr