spocc: Interface to Species Occurrence Data Sources

種の分布情報を取得するパッケージ

> library(spocc)

バージョン: 0.4.5

関数名 概略
as.antweb Coerce occurrence keys to antwebkey/occkey objects
as.bison Coerce occurrence keys to bisonkey/occkey objects
as.ecoengine Coerce occurrence keys to ecoenginekey/occkey objects
as.gbif Coerce occurrence keys to gbifkey/occkey objects
as.idigbio Coerce occurrence keys to idigbio uuid objects
as.inat Coerce occurrence keys to iNaturalist id objects
as.vertnet Coerce occurrence keys to vertnetkey/occkey objects
bbox2wkt Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
fixnames Change names to be the same for each taxon.
inspect Get more data on individual occurrences.
occ Search for species occurrence data across many data sources.
occ2df Combine results from occ calls to a single data.frame
occ_names Search for species names across many data sources.
occ_names_options Look up options for parameters passed to each source for occ_names function
occ_options Look up options for parameters passed to each source
spocc-package R interface to many species occurrence data sources
spocc_duplicates A note about duplicate occurrence records
wkt Read or write WKT
wkt_vis Visualize well-known text area's on a map.

fixnames

Arguments

  • obj... occdataクラスオブジェクト
  • how... shortest, query, supplied
  • namevec
> fixnames(obj, how = "shortest", namevec = NULL)

inspect

> inspect(x, from = "gbif")

occ

生物情報データから種データの検索

Arguments

  • query
  • from
  • limit
  • start, page
  • geometry... 地理範囲の指定
  • has_coords... 位置情報を含む
  • ids
  • callopts
  • gbifopts... GBIFのデータを検索する際のオプション指定
  • bisonopts
  • inatopts
  • ebirdopts
  • ecoengineopts
  • antwebopts
  • vertnetopts
  • idigbioopts
> occ(query = NULL, from = "gbif", limit = 500, start = NULL,
+   page = NULL, geometry = NULL, has_coords = NULL, ids = NULL,
+   callopts = list(), gbifopts = list(), bisonopts = list(),
+   inatopts = list(), ebirdopts = list(), ecoengineopts = list(),
+   antwebopts = list(), vertnetopts = list(), idigbioopts = list())

occ2df

> c('Accipiter striatus', 'Setophaga caerulescens', 'Carduelis tristis') %>% 
+   occ(query = ., from = 'gbif', gbifopts = list(hasCoordinate = TRUE), limit = 10) %>% 
+   occ2df()

occ_options

検索するデータベースの設定

Arguments

  • from
  • where... console, html
> occ_options(from = "gbif", where = "html")