SP2000-package {SP2000}

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 = "[e-mail]", role = c("aut", "cre"), comment = c(ORCID="0000-0002-5490-182X")), person(given = "Minrui", family = "Huang", email = "[e-mail]", role = "ctb"), person(given = "Ke", family = "Yang", email = "[e-mail]", role = "ctb"), person(given = "Jun", family = "Wang", email = "[e-mail]", role = "ctb", comment = c(ORCID="0000-0003-2481-1409")), person(given = "Juan", family = "Tao", email = "[e-mail]", role = "ctb"), person(given = "Chengzhi", family = "Ding", email = "[e-mail]", role = "ctb", comment = c(ORCID="0000-0001-5215-7374")), person(given = "Daming", family = "He", email = "[e-mail]", role = "ctb") )
Maintainer:	Liuyong Ding <[e-mail]>
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 <[e-mail]>

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)