SP2000-package {SP2000} | R Documentation |
Catalogue of Life Toolkit
Description
This package is designed for mining the checklist of animals, plants, fungi and micro-organisms both in and outside China.
Details
Package: | SP2000 |
Type: | Package |
Title: | Catalogue of Life Toolkit |
Version: | 0.2.0 |
Date: | 2020-10-26 |
Authors@R: | c( person(given = "Liuyong", family = "Ding", email = "ly_ding@126.com", role = c("aut", "cre"), comment = c(ORCID="0000-0002-5490-182X")), person(given = "Minrui", family = "Huang", email = "minrui-huang@mail.ynu.edu.cn", role = "ctb"), person(given = "Ke", family = "Yang", email = "ydyangke@163.com", role = "ctb"), person(given = "Jun", family = "Wang", email = "wangjun168@ynu.edu.cn", role = "ctb", comment = c(ORCID="0000-0003-2481-1409")), person(given = "Juan", family = "Tao", email = "taojuanat@gmail.com", role = "ctb"), person(given = "Chengzhi", family = "Ding", email = "chzhding@ynu.edu.cn", role = "ctb", comment = c(ORCID="0000-0001-5215-7374")), person(given = "Daming", family = "He", email = "dmhe@ynu.edu.cn", role = "ctb") ) |
Maintainer: | Liuyong Ding <ly_ding@126.com> |
Description: | A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org>, China animal scientific database <http://zoology.especies.cn> and catalogue of life Taiwan <https://taibnet.sinica.edu.tw/home_eng.php>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China <2019HJ2096001006>,Yunnan University's "Double First Class" Project <C176240405> and Yunnan University's Research Innovation Fund for Graduate Students <2019227>. |
Depends: | R (>= 3.0.0) |
Imports: | jsonlite, tibble, pbmcapply, purrr, rlist, XML, xml2, DT, urltools |
Suggests: | utils, testthat |
License: | Artistic-2.0 |
URL: | https://otoliths.github.io/SP2000/ |
BugReports: | https://github.com/Otoliths/SP2000/issues |
Encoding: | UTF-8 |
LazyData: | true |
RoxygenNote: | 7.1.1 |
Author: | Liuyong Ding [aut, cre] (<https://orcid.org/0000-0002-5490-182X>), Minrui Huang [ctb], Ke Yang [ctb], Jun Wang [ctb] (<https://orcid.org/0000-0003-2481-1409>), Juan Tao [ctb], Chengzhi Ding [ctb] (<https://orcid.org/0000-0001-5215-7374>), Daming He [ctb] |
Index of help topics:
SP2000-package Catalogue of Life Toolkit download_col_china Download 'Catalogue of Life China': Annual Checklist find_synonyms Find synonyms via species name get_col_global Search Catalogue of Life Global checklist get_col_taiwan Search Catalogue of Life Taiwan checklist get_province Statistics on Species or Infraspecies by Province from Catalogue of Life China checklist get_redlist_china Query Redlist of Chinese Biodiversity get_top20 Download the top20 species for Catalogue of Life China checklist list_df Catalogue of Life list(s) convert data frame open_url Opening the Catalogue of Life China checklist web pages with query search_checklist Search Catalogue of Life China checklist search_family_id Search family IDs search_taxon_id Search taxon IDs set_search_key SP2000 API keys zoology_dbase_name Query details of species in China Animal Scientific Database zoology_description Query details of species in China Animal Scientific Database
Author(s)
Maintainer: Liuyong Ding <ly_ding@126.com>
References
Ding LY, Li H, Tao J, Zhang JL, Huang MR, Yang K, Wang J, He DM, Ding CZ (2020) SP2000: An open-sourced R package for querying the Catalogue of Life. Biodiversity Science.
https://cran.r-project.org/package=SP2000
https://pypi.org/project/SP2000
Examples
## Not run:
# Note: You need to apply for the apiKey <http://sp2000.org.cn/api/document>
to run search_* functions of this package.
## Load "SP2000"
library('SP2000')
## Set your key
set_search_key("your apiKey",db = "sp2000")
## Search family IDs via family name, supports Latin and Chinese names
familyid <- search_family_id(query = "Anguillidae")
## Search taxon IDs via familyID ,scientificName and commonName
query <- familyid$Anguillidae$data$record_id
taxonid <- search_taxon_id(query = query,name = "familyID")
queries = c("Anguilla marmorata","Anguilla japonica",
"Anguilla bicolor","Anguilla nebulosa",
"Anguilla luzonensis")
search_taxon_id(query = queries,name = "scientificName")
## Download detailed lists via species or infraspecies ID
query <- taxonid[["3851c5311bed46c19529cb155d37aa9b"]][["data"]][["namecode"]]
checklist <- search_checklist(query = query)
## Get Catalogue of Life Global checklist via species name and id
x <- get_col_global(query = "Anguilla", response = "full")
str(x)
x[["Anguilla"]][["meta"]][["total_number_of_results"]] [1]
## Find synonyms via species name from Catalogue of Life Global
find_synonyms(query = queries)
## Search Catalogue of Life Taiwan checklist
get_col_taiwan(query = "Anguillidae", level = "family")
## Query Redlist of Chinese Biodiversity
get_redlist_china(query = "Anguilla", option = "Scientific Names")
## End(Not run)
[Package SP2000 version 0.2.0 Index]