antweb removed

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Interface to Species Occurrence Data Sources
 Description: A programmatic interface to many species occurrence data sources,
     including Global Biodiversity Information Facility ('GBIF'), 'USGSs'
     Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist',
-    Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized
+    Berkeley 'Ecoinformatics' Engine, 'eBird', Integrated Digitized
     'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information
     System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
     functionality for retrieving species occurrence data, and combining

NAMESPACE

@@ -6,12 +6,6 @@ S3method(as.ala,data.frame)
 S3method(as.ala,list)
 S3method(as.ala,occdat)
 S3method(as.ala,occkey)
-S3method(as.antweb,antwebkey)
-S3method(as.antweb,character)
-S3method(as.antweb,data.frame)
-S3method(as.antweb,list)
-S3method(as.antweb,occdat)
-S3method(as.antweb,occkey)
 S3method(as.bison,bisonkey)
 S3method(as.bison,character)
 S3method(as.bison,data.frame)
@@ -68,7 +62,6 @@ S3method(print,occnames)
 S3method(summary,occdat)
 S3method(summary,occdatind)
 export(as.ala)
-export(as.antweb)
 export(as.bison)
 export(as.ecoengine)
 export(as.gbif)

R/inspect.R

@@ -5,7 +5,7 @@
 #' @param x The output from \code{\link{occ}} call, output from call to
 #' \code{\link{occ2df}}, or an occurrence ID as a occkey class.
 #' @param from  (character) The data provider. One of gbif, bison, inat,
-#' antweb, ecoengine, or vertnet
+#' ecoengine, or vertnet
 #' @return A list, with each slot named for the data source, and then
 #' within data sources is a slot for each taxon, named by it's occurrence ID.
 #'
@@ -52,7 +52,6 @@ inspect.occkey <- function(x, from="gbif"){
          gbifkey = as.gbif(x),
          bisonkey = as.bison(x),
          ecoenginekey = as.ecoengine(x),
-         antwebkey = as.antweb(x),
          idigbiokey = as.idigbio(x))
 }
 
@@ -65,7 +64,6 @@ make_df <- function(x){
              gbif = as.gbif(obj[[i]]),
              bison = as.bison(obj[[i]]),
              ecoengine = as.ecoengine(obj[[i]]),
-             antweb = as.antweb(obj[[i]]),
              idigbio = as.idigbio(obj[[i]])
       )
   }

R/occ.r

@@ -11,7 +11,7 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
   page = NULL, geometry = NULL, has_coords = NULL, ids = NULL, date = NULL,
   callopts=list(),
   gbifopts = list(), bisonopts = list(), inatopts = list(),
-  ebirdopts = list(), ecoengineopts = list(), antwebopts = list(),
+  ebirdopts = list(), ecoengineopts = list(),
   vertnetopts = list(), idigbioopts = list(), obisopts = list(), 
   alaopts = list()) {
 
@@ -39,7 +39,7 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
     }
   }
   sources <- match.arg(from, choices = c("gbif", "bison", "inat", "ebird",
-            "ecoengine", "antweb", "vertnet", "idigbio", "obis", "ala"),
+            "ecoengine", "vertnet", "idigbio", "obis", "ala"),
                        several.ok = TRUE)
   if (!all(from %in% sources)) {
     stop(
@@ -63,13 +63,12 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
     inat_res <- foo_inat(sources, x, y, p, z, hc, d, w, inatopts)
     ebird_res <- foo_ebird(sources, x, y, w, ebirdopts)
     ecoengine_res <- foo_ecoengine(sources, x, y, p, z, hc, d, w, ecoengineopts)
-    antweb_res <- foo_antweb(sources, x, y, s, z, hc, d, w, antwebopts)
     vertnet_res <- foo_vertnet(sources, x, y, hc, d, w, vertnetopts)
     idigbio_res <- foo_idigbio(sources, x, y, s, z, hc, d, w, idigbioopts)
     obis_res <- foo_obis(sources, x, y, s, z, hc, d, w, obisopts)
     ala_res <- foo_ala(sources, x, y, s, z, hc, d, w, alaopts)
     list(gbif = gbif_res, bison = bison_res, inat = inat_res, ebird = ebird_res,
-         ecoengine = ecoengine_res, antweb = antweb_res, vertnet = vertnet_res,
+         ecoengine = ecoengine_res, vertnet = vertnet_res,
          idigbio = idigbio_res, obis = obis_res, ala = ala_res)
   }
 
@@ -90,7 +89,6 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
          inat = list(time = NULL, data = data_frame()),
          ebird = list(time = NULL, data = data_frame()),
          ecoengine = list(time = NULL, data = data_frame()),
-         antweb = list(time = NULL, data = data_frame()),
          vertnet = list(time = NULL, data = data_frame()),
          idigbio = list(time = NULL, data = data_frame()),
          obis = list(time = NULL, data = data_frame()),
@@ -259,13 +257,12 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
   inat_sp <- getsplist("inat", inatopts)
   ebird_sp <- getsplist("ebird", ebirdopts)
   ecoengine_sp <- getsplist("ecoengine", ecoengineopts)
-  antweb_sp <- getsplist("antweb", antwebopts)
   vertnet_sp <- getsplist("vertnet", vertnetopts)
   idigbio_sp <- getsplist("idigbio", idigbioopts)
   obis_sp <- getsplist("obis", obisopts)
   ala_sp <- getsplist("ala", alaopts)
   p <- list(gbif = gbif_sp, bison = bison_sp, inat = inat_sp, ebird = ebird_sp,
-            ecoengine = ecoengine_sp, antweb = antweb_sp, vertnet = vertnet_sp,
+            ecoengine = ecoengine_sp, vertnet = vertnet_sp,
             idigbio = idigbio_sp, obis = obis_sp, ala = ala_sp)
   structure(p, class = "occdat", searched = from)
 }

R/occ2df.R

@@ -21,9 +21,6 @@
 #'  \item key - occurrence record key
 #' }
 #'
-#' AntWeb doesn't provide dates, so occurrence rows from that provider
-#' are blank.
-#'
 #' @examples \dontrun{
 #' # combine results from output of an occ() call
 #' spnames <- c('Accipiter striatus', 'Setophaga caerulescens',
@@ -74,7 +71,6 @@ occ2df.occdat <- function(obj, what = "data") {
   cc <- foolist(obj$inat)
   dd <- foolist(obj$ebird)
   ee <- foolist(obj$ecoengine)
-  aw <- foolist(obj$antweb)
   vn <- foolist(obj$vertnet)
   id <- foolist(obj$idigbio)
   ob <- foolist(obj$obis)
@@ -97,26 +93,26 @@ occ2df.occdat <- function(obj, what = "data") {
           rename(dat, stats::setNames("key", keymap[[y]]))
         }
       },
-      list(aa, bb, cc, dd, ee, aw, vn, id, ob, ala),
-      c('gbif','bison','inat','ebird','ecoengine','antweb',
+      list(aa, bb, cc, dd, ee, vn, id, ob, ala),
+      c('gbif','bison','inat','ebird','ecoengine',
         'vertnet','idigbio','obis','ala')
     )
   )
   tmpout <- list(
     meta = list(obj$gbif$meta, obj$bison$meta, obj$inat$meta,
-                obj$ebird$meta, obj$ecoengine$meta, obj$aw$meta, obj$vn$meta,
+                obj$ebird$meta, obj$ecoengine$meta, obj$vn$meta,
                 obj$id$meta, obj$ob$meta, obj$ala$meta),
     data = tmp
   )
   if (what %in% "data") as_data_frame(tmpout$data) else tmpout
 }
 
 datemap <- list(gbif = 'eventDate', bison = 'date', inat = 'observed_on',
-                ebird = 'obsDt', ecoengine = 'begin_date', antweb = NULL,
+                ebird = 'obsDt', ecoengine = 'begin_date',
                 vertnet = "eventdate", idigbio = "datecollected",
                 obis = "eventDate", ala = "eventDate")
 
 keymap <- list(gbif = "key", bison = "occurrenceID", inat = "id",
-               ebird = "locID", ecoengine = "key", antweb = "catalogNumber",
+               ebird = "locID", ecoengine = "key",
                vertnet = "occurrenceid", idigbio = "uuid", obis = "id",
                ala = "uuid")

R/occ_options.r

@@ -20,16 +20,14 @@
 #' strings too (e.g., 'rv' for 'rvertnet').
 #' 
 #' For some data sources we don't import the canonical package, but instead
-#' have our own intenral helper functions and the package in question is
+#' have our own internal helper functions and the package in question is
 #' not imported, but we do suggest seeing the help for the package on 
 #' their parameters:
 #' 
 #' \itemize{
-#'  \item **AntWeb**: `?AntWeb::aw_data`
 #'  \item **ecoengine**: `?ecoengine::ee_observations`
 #' }
 #' 
-#' For others, 
 #' @examples \dontrun{
 #' # opens up documentation for this function
 #' occ_options()

R/plugins.r

@@ -149,55 +149,6 @@ foo_ecoengine <- function(sources, query, limit, page, geometry, has_coords,
   }
 }
 
-
-#' @noRd
-foo_antweb <- function(sources, query, limit, start, geometry, has_coords,
-                       date, callopts, opts) {
-  if (any(grepl("antweb", sources))) {
-    time <- now()
-    opts$georeferenced <- has_coords
-    # limit <- NULL
-    geometry <- NULL
-
-    query <- sub("^ +", "", query)
-    query <- sub(" +$", "", query)
-
-    if (length(strsplit(query, " ")[[1]]) == 2) {
-      opts$scientific_name <- query
-    } else {
-      opts$genus <- query
-      opts$scientific_name <- NULL
-    }
-
-    if (!is.null(date)) {
-      if (length(date) != 2) stop("'date' for Ecoengine must be length 2")
-      opts$min_date <- date[1]
-      opts$max_date <- date[2]
-    }
-
-    if (!'limit' %in% names(opts)) opts$limit <- limit
-    if (!'offset' %in% names(opts)) opts$offset <- start
-    if (length(callopts) > 0) opts$callopts <- callopts
-    out <- tryCatch(do.call(aw_data2, opts), error = function(e) e)
-
-    if (is.null(out) || inherits(out, "simpleError") || NROW(out$data) == 0) {
-      warning(sprintf("No records found in AntWeb for %s", query),
-              call. = FALSE)
-      emptylist(opts)
-    } else {
-      res <- out$data
-      res$prov <- rep("antweb", nrow(res))
-      res$name <- query
-      res <- stand_latlon(res)
-      res <- add_latlong_if_missing(res)
-      list(time = time, found = out$count, data = as_data_frame(res),
-           opts = opts)
-    }
-  } else {
-    emptylist(opts)
-  }
-}
-
 #' @noRd
 foo_bison <- function(sources, query, limit, start, geometry, date, 
   callopts, opts) {