Remove USGS BISON via the package rbison as a data source in spocc

DESCRIPTION

@@ -1,14 +1,12 @@
 Package: spocc
 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',
-    '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
-    those data.
-Version: 1.2.0.91
+    including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist',
+    '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 those data.
+Version: 1.2.1.91
 License: MIT + file LICENSE
 Authors@R: 
     c(person(given = "Hannah", family = "Owens",
@@ -36,7 +34,6 @@ Language: en-US
 Imports:
     utils,
     rgbif,
-    rbison,
     rebird,
     rvertnet,
     ridigbio,
@@ -51,7 +48,7 @@ Suggests:
     testthat,
     taxize,
     vcr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
 X-schema.org-applicationCategory: Biodiversity
 X-schema.org-keywords: specimens, API, web-services, occurrences, species, taxonomy, GBIF, INAT, BISON, Vertnet, eBird, iDigBio, OBIS, ALA
 X-schema.org-isPartOf: https://ropensci.org

NAMESPACE

@@ -6,13 +6,6 @@ S3method(as.ala,data.frame)
 S3method(as.ala,list)
 S3method(as.ala,occdat)
 S3method(as.ala,occkey)
-S3method(as.bison,bisonkey)
-S3method(as.bison,character)
-S3method(as.bison,data.frame)
-S3method(as.bison,list)
-S3method(as.bison,numeric)
-S3method(as.bison,occdat)
-S3method(as.bison,occkey)
 S3method(as.gbif,character)
 S3method(as.gbif,data.frame)
 S3method(as.gbif,gbifkey)
@@ -56,7 +49,6 @@ S3method(print,occnames)
 S3method(summary,occdat)
 S3method(summary,occdatind)
 export(as.ala)
-export(as.bison)
 export(as.ecoengine)
 export(as.gbif)
 export(as.idigbio)
@@ -84,9 +76,6 @@ importFrom(lubridate,ydm_hm)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hm)
 importFrom(lubridate,ymd_hms)
-importFrom(rbison,bison)
-importFrom(rbison,bison_solr)
-importFrom(rbison,bison_tax)
 importFrom(rebird,ebirdgeo)
 importFrom(rebird,ebirdregion)
 importFrom(rgbif,name_lookup)

R/inspect.R

@@ -9,14 +9,14 @@
 #' @export
 #' @param x The output from [occ()] call, output from call to
 #' [occ2df()], or an occurrence ID as a occkey class.
-#' @param from (character) The data provider. One of gbif, bison, inat,
+#' @param from (character) The data provider. One of gbif, inat,
 #' 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.
 #'
 #' @examples \dontrun{
 #' spnames <- c('Accipiter striatus', 'Spinus tristis')
-#' out <- occ(query=spnames, from=c('gbif','bison'),
+#' out <- occ(query=spnames, from=c('gbif','idigbio'),
 #'    gbifopts=list(hasCoordinate=TRUE), limit=2)
 #' res <- occ2df(out)
 #' inspect(res)
@@ -55,7 +55,6 @@ inspect.occdat <- function(x, from="gbif") {
 inspect.occkey <- function(x, from="gbif"){
   switch(class(x)[1],
          gbifkey = as.gbif(x),
-         bisonkey = as.bison(x),
          idigbiokey = as.idigbio(x))
 }
 
@@ -66,7 +65,6 @@ make_df <- function(x){
     out[[ names(obj)[i] ]] <-
       switch(names(obj)[i],
              gbif = as.gbif(obj[[i]]),
-             bison = as.bison(obj[[i]]),
              idigbio = as.idigbio(obj[[i]])
       )
   }

R/occ.r

@@ -10,7 +10,7 @@
 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(),
+  gbifopts = list(), inatopts = list(),
   ebirdopts = list(), vertnetopts = list(), idigbioopts = list(),
   obisopts = list(), alaopts = list(), throw_warnings = TRUE) {
 
@@ -29,12 +29,12 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
   type <- "sci"
 
   geometry <- occ_geom(geometry)
-  sources <- match.arg(from, choices = c("gbif", "bison", "inat", "ebird",
+  sources <- match.arg(from, choices = c("gbif", "inat", "ebird",
     "vertnet", "idigbio", "obis", "ala"),
     several.ok = TRUE)
 
   # collect all data sources opts into named list to index to later
-  ds <- list(gbif=gbifopts, bison=bisonopts, inat=inatopts,
+  ds <- list(gbif=gbifopts, inat=inatopts,
     ebird=ebirdopts, vertnet=vertnetopts,
     idigbio=idigbioopts, obis=obisopts, ala=alaopts)
 
@@ -80,7 +80,7 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
   } else if (is.null(query) && is.null(geometry) && !is.null(ids)) {
     ids <- occ_unlistids(ids)
     # if ids is not null (taxon identifiers passed in)
-    # ids can only be passed to gbif and bison for now
+    # ids can only be passed to gbif for now
     # so don't pass anything on to inat or ebird
     tmp <- lapply(ids, occ_loopids, y = limit, s = start, p = page,
       z = geometry, hc = has_coords, d = date, w = callopts,
@@ -106,8 +106,6 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
 
   gbif_sp <- occ_getsplist(tmp, "gbif", sources, type, ds$gbif, query, geometry,
     ids)
-  bison_sp <- occ_getsplist(tmp, "bison", sources, type, ds$bison, query, geometry,
-    ids)
   inat_sp <- occ_getsplist(tmp, "inat", sources, type, ds$inat, query, geometry,
     ids)
   ebird_sp <- occ_getsplist(tmp, "ebird", sources, type, ds$ebird, query, geometry,
@@ -120,7 +118,7 @@ occ <- function(query = NULL, from = "gbif", limit = 500, start = NULL,
     ids)
   ala_sp <- occ_getsplist(tmp, "ala", sources, type, ds$ala,
     query, geometry, ids)
-  p <- list(gbif = gbif_sp, bison = bison_sp, inat = inat_sp, ebird = ebird_sp,
+  p <- list(gbif = gbif_sp, inat = inat_sp, ebird = ebird_sp,
             vertnet = vertnet_sp, idigbio = idigbio_sp, obis = obis_sp,
             ala = ala_sp)
   structure(p, class = "occdat", searched = from)

R/occ2df.R

@@ -30,10 +30,10 @@
 #'
 #' out <- occ(
 #'   query='Accipiter striatus',
-#'   from=c('gbif','bison','ebird','inat'),
+#'   from=c('gbif','ebird','inat'),
 #'   gbifopts=list(hasCoordinate=TRUE), limit=2)
 #' occ2df(out)
-#' occ2df(out$bison)
+#' occ2df(out$gbif)
 #'
 #' # or combine many results from a single data source
 #' spnames <- c('Accipiter striatus', 'Spinus tristis')
@@ -61,7 +61,6 @@ foolist <- function(x) {
 occ2df.occdat <- function(obj, what = "data") {
   what <- match.arg(what, choices = c("all", "data"))
   aa <- foolist(obj$gbif)
-  bb <- foolist(obj$bison)
   cc <- foolist(obj$inat)
   dd <- foolist(obj$ebird)
   vn <- foolist(obj$vertnet)
@@ -86,25 +85,25 @@ occ2df.occdat <- function(obj, what = "data") {
           rename(dat, stats::setNames("key", keymap[[y]]))
         }
       },
-      list(aa, bb, cc, dd, vn, id, ob, ala),
-      c('gbif','bison','inat','ebird',
+      list(aa, cc, dd, vn, id, ob, ala),
+      c('gbif','inat','ebird',
         'vertnet','idigbio','obis','ala')
     )
   )
   tmpout <- list(
-    meta = list(obj$gbif$meta, obj$bison$meta, obj$inat$meta,
+    meta = list(obj$gbif$meta, obj$inat$meta,
                 obj$ebird$meta, obj$vn$meta, obj$id$meta,
                 obj$ob$meta, obj$ala$meta),
     data = tmp
   )
   if (what %in% "data") as_tibble(tmpout$data) else tmpout
 }
 
-datemap <- list(gbif = 'eventDate', bison = 'date', inat = 'observed_on',
+datemap <- list(gbif = 'eventDate', inat = 'observed_on',
                 ebird = 'obsDt', vertnet = "eventdate",
                 idigbio = "datecollected", obis = "eventDate",
                 ala = "eventDate")
 
-keymap <- list(gbif = "key", bison = "occurrenceID", inat = "id",
+keymap <- list(gbif = "key", inat = "id",
                ebird = "locID", vertnet = "occurrenceid", idigbio = "uuid",
                obis = "id", ala = "uuid")

R/occ_funs.R

@@ -6,14 +6,13 @@ occ_loopfun <- function(x, y, s, p, z, hc, d, w, sources, ds) {
   # x = query; y = limit; s = start; p = page;
   # z = geometry; hc = has_coords; d = date; w = callopts
   gbif_res <- foo_gbif(sources, x, y, s, z, hc, d, w, ds$gbif)
-  bison_res <- foo_bison(sources, x, y, s, z, d, w, ds$bison)
   inat_res <- foo_inat(sources, x, y, p, z, hc, d, w, ds$inat)
   ebird_res <- foo_ebird(sources, x, y, w, ds$ebird)
   vertnet_res <- foo_vertnet(sources, x, y, hc, d, w, ds$vertnet)
   idigbio_res <- foo_idigbio(sources, x, y, s, z, hc, d, w, ds$idigbio)
   obis_res <- foo_obis(sources, x, y, s, z, hc, d, w, ds$obis)
   ala_res <- foo_ala(sources, x, y, s, z, hc, d, w, ds$ala)
-  list(gbif = gbif_res, bison = bison_res, inat = inat_res, ebird = ebird_res,
+  list(gbif = gbif_res, inat = inat_res, ebird = ebird_res,
        vertnet = vertnet_res,
        idigbio = idigbio_res, obis = obis_res, ala = ala_res)
 }
@@ -25,13 +24,11 @@ occ_loopids <- function(x, y, s, p, z, hc, d, w, sources, ds) {
          call. = FALSE)
   if (inherits(x, 'gbifid')) {
     gbif_res <- foo_gbif(sources, x, y, s, z, hc, d, w, ds$gbif)
-    bison_res <- empty_time_data()
   } else if (inherits(x, 'tsn')) {
-    bison_res <- foo_bison(sources, x, y, s, z, d, w, ds$bison)
     gbif_res <- empty_time_data()
+    warning("bison no longer supported", call. = FALSE)
   }
   list(gbif = gbif_res,
-       bison = bison_res,
        inat = empty_time_data(),
        ebird = empty_time_data(),
        vertnet = empty_time_data(),