Package 'SP2000' reference manual

Title:	Catalogue of Life Toolkit
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>.
Authors:	Liuyong Ding [aut, cre] , Minrui Huang [ctb], Ke Yang [ctb], Jun Wang [ctb] , Juan Tao [ctb], Chengzhi Ding [ctb] , Daming He [ctb]
Maintainer:	Liuyong Ding <[email protected]>
License:	Artistic-2.0
Version:	0.2.0
Built:	2025-02-21 03:29:23 UTC
Source:	https://github.com/otoliths/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 = "[email protected]", role = c("aut", "cre"), comment = c(ORCID="0000-0002-5490-182X")), person(given = "Minrui", family = "Huang", email = "[email protected]", role = "ctb"), person(given = "Ke", family = "Yang", email = "[email protected]", role = "ctb"), person(given = "Jun", family = "Wang", email = "[email protected]", role = "ctb", comment = c(ORCID="0000-0003-2481-1409")), person(given = "Juan", family = "Tao", email = "[email protected]", role = "ctb"), person(given = "Chengzhi", family = "Ding", email = "[email protected]", role = "ctb", comment = c(ORCID="0000-0001-5215-7374")), person(given = "Daming", family = "He", email = "[email protected]", role = "ctb") )
Maintainer:	Liuyong Ding <[email protected]>
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
Config/pak/sysreqs:	make libxml2-dev zlib1g-dev
Repository:	https://otoliths.r-universe.dev
RemoteUrl:	https://github.com/otoliths/sp2000
RemoteRef:	HEAD
RemoteSha:	bce8056d4c4788bc0b51b71e9ba81b771d312d73
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 <[email protected]>

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)
## 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)

Download 'Catalogue of Life China': Annual Checklist

Description

Organized by the Biodiversity Committee of Chinese Academy of Sciences (BC-CAS), Catalogue of Life China Annual Checklist edition has been compiled by Species 2000 China Node.

Usage

download_col_china(version = "2020", OS = "MacOS", dir = tempdir(), mode, ...)
download_col_china(version = "2020", OS = "MacOS", dir = tempdir(), mode, ...)

Arguments

`version`	`integer` Release version of annual checklist,the default value is 2020.
`OS`	`character` Supported operating system,c("MacOS", "Ubuntu" ,"Windows"),the default value is "MacOS".
`dir`	A non-empty character vector giving the directory name by user,the default value is dir = tempdir(),see `tempdir` for details.
`mode`	A character string specifying the mode with which to write the file. Useful values are "w", "wb" (binary), "a" (append) and "ab". see `download.file` for details.
`...`	Allow additional arguments to be passed, unused. see `download.file` for details.

Details

Visit the website http://sp2000.org.cn/download for more details.

Value

URL

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
dir <- tempdir()
download_col_china(version = "2020",OS = "MacOS", dir = dir)

## End(Not run)
## Not run: 
dir <- tempdir()
download_col_china(version = "2020",OS = "MacOS", dir = dir)

## End(Not run)

Find synonyms via species name

Description

Find synonyms via species name from Catalogue of Life Global.

Usage

find_synonyms(query, mc.cores = 2)
find_synonyms(query, mc.cores = 2)

Arguments

`query`	`character` species name,The function is similar to `get_col_global`.
`mc.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized from environment variable MC_CORES if set. Must be at least one, and parallelization requires at least two cores,see `mclapply` for details.

Details

Visit the website http://webservice.catalogueoflife.org/col/webservice for more details.

Value

object

Author(s)

Liuyong Ding [email protected]

References

https://github.com/lutteropp/SpeciesSynonymFinder/blob/master/find_synonyms.r

Examples

## Not run: 
##Get Catalogue of Life Global checklist via species name
x1 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                              "Anguilla bicolor","Anguilla nebulosa",
                              "Anguilla luzonensis"),
                               option = "name")
str(x1)

##full queries
x2 <- get_col_global(query = "Anguilla", response = "full")


##Find synonyms via species name
find_synonyms(query = c("Anguilla marmorata","Anguilla japonica",
                        "Anguilla bicolor","Anguilla nebulosa",
                        "Anguilla luzonensis"))

## End(Not run)
## Not run: 
##Get Catalogue of Life Global checklist via species name
x1 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                              "Anguilla bicolor","Anguilla nebulosa",
                              "Anguilla luzonensis"),
                               option = "name")
str(x1)

##full queries
x2 <- get_col_global(query = "Anguilla", response = "full")


##Find synonyms via species name
find_synonyms(query = c("Anguilla marmorata","Anguilla japonica",
                        "Anguilla bicolor","Anguilla nebulosa",
                        "Anguilla luzonensis"))

## End(Not run)

Search Catalogue of Life Global checklist

Description

Get Catalogue of Life Global checklist via species name and id.

Usage

get_col_global(
  query,
  option = "name",
  response = "terse",
  start = 0,
  limit = 500,
  mc.cores = 2
)
get_col_global(
  query,
  option = "name",
  response = "terse",
  start = 0,
  limit = 500,
  mc.cores = 2
)

Arguments

`query`	`string` The string to search for.
`option`	`character` There is one required parameter, which is either name or id. Give eithera name or an ID. If an ID is given, the name parameter may not be used, and vice versa. option=c("id","name"),the default value is "name". Only exact matches found the name given will be returned, unless a wildcard () is appended. Wildcards are allowed only at the end of the string. This offers the option to e.g. search for genus to retrieve the genus plus all its (infra)species. The name must be at least 3 characters long, not counting the wildcard character. The record ID of the specific record to return (only for scientific names of species or infraspecific taxa).
`response`	`character` Type of response returned. Valid values are response=terse and response=full. if the response parameter is omitted, the results are returned in the default terse format. If format=terse then a minimum set of results are returned (this is faster and smaller, enough for name lookup), if format=full then all available information is returned, response=c("full","terse"),the default value is "terse".
`start`	`integer` Record number to start at. If omitted, the results are returned from the first record (start=0). Use in combination with limit to page through results. Note that we do the paging internally for you, but you can manually set the start parameter.
`limit`	`integer` Number of records to return. This is useful if the total number of results is larger than the maximum number of results returned by a single Web service query (currently the maximum number of results returned by a single query is 500 for terse queries and 50 for full queries,the default value is 500.Note that there is a hard maximum of 10,000, which is calculated as the limit+start, so start=99,00 and limit=2000 won't work.
`mc.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized from environment variable MC_CORES if set. Must be at least one, and parallelization requires at least two cores,see `mclapply` for details.

Details

Visit the website http://webservice.catalogueoflife.org/col/webservice for more details.

Value

object

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Get Catalogue of Life Global checklist via species name
x1 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                              "Anguilla bicolor","Anguilla nebulosa",
                              "Anguilla luzonensis"),
                               option = "name")
str(x1)

##full queries
x2 <- get_col_global(query = "Anguilla", response = "full")


##Find synonyms via species name
find_synonyms(query = c("Anguilla marmorata","Anguilla japonica",
                        "Anguilla bicolor","Anguilla nebulosa",
                        "Anguilla luzonensis"))

## End(Not run)
## Not run: 
##Get Catalogue of Life Global checklist via species name
x1 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                              "Anguilla bicolor","Anguilla nebulosa",
                              "Anguilla luzonensis"),
                               option = "name")
str(x1)

##full queries
x2 <- get_col_global(query = "Anguilla", response = "full")


##Find synonyms via species name
find_synonyms(query = c("Anguilla marmorata","Anguilla japonica",
                        "Anguilla bicolor","Anguilla nebulosa",
                        "Anguilla luzonensis"))

## End(Not run)

Search Catalogue of Life Taiwan checklist

Description

Get Catalogue of Life Taiwan checklist via advanced query.

Usage

get_col_taiwan(
  query,
  level = "species",
  option = "equal",
  include_synonyms = TRUE
)
get_col_taiwan(
  query,
  level = "species",
  option = "equal",
  include_synonyms = TRUE
)

Arguments

`query`	`string` The string to search for.
`level`	`character` Query by category level, level=c("kingdom","phylum","class","order","family","genus","species"),the default value is "species".
`option`	`character` Query format, option=c("contain","equal","beginning"),the default value is "equal".
`include_synonyms`	`logic` Whether the results contain a synonym or not.

Details

Visit the website https://taibnet.sinica.edu.tw/eng/taibnet_species_query.php for more details.

Value

object

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Search Catalogue of Life Taiwan checklist
get_col_taiwan(query="Anguilla",level="species",option = "contain")

get_col_taiwan(query="Anguillidae",level="family")

## End(Not run)
## Not run: 
##Search Catalogue of Life Taiwan checklist
get_col_taiwan(query="Anguilla",level="species",option = "contain")

get_col_taiwan(query="Anguillidae",level="family")

## End(Not run)

Statistics on Species or Infraspecies by Province from Catalogue of Life China checklist

Description

Download the statistics datasets on species/infraspecies by province at http://sp2000.org.cn/statistics/statistics_map for more details.

Usage

get_province()
get_province()

Details

Visit the website http://sp2000.org.cn/statistics/statistics_map for more details.

Value

Statistics on species or infraspecies by province.

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
get_province()


## End(Not run)
## Not run: 
get_province()


## End(Not run)

Query Redlist of Chinese Biodiversity

Description

Query Redlist of China’s Biodiversity of Vertebrate, Higher Plants and Macrofungi.

Usage

get_redlist_china(
  query = NULL,
  option = "Scientific Names",
  group = "Amphibians",
  viewDT = FALSE
)
get_redlist_china(
  query = NULL,
  option = "Scientific Names",
  group = "Amphibians",
  viewDT = FALSE
)

Arguments

`query`	`string` The string to query for.
`option`	`character` There is one required parameter, which is either Chinese Names or Scientific Names. Give eithera Chinese Names or Scientific Names. If an Scientific Names is given, the Chinese Names parameter may not be used. Only exact matches found the name given will be returned. option=c("Chinese Names","Scientific Names"),,the default value is "Scientific Names".
`group`	`character` There is one required parameter, group=c("Amphibians","Birds","Inland Fishes","Mammals","Reptiles","Plants","Fungi").
`viewDT`	`logic` TRUE or FALSE,the default value is FALSE.

Format

assessment status:

EX: Extinct
EW: Extinct in the wild
RE: Regional Extinct
CR: Critically Endangered
EN: Endangered
VU: Vulnerable
NT: Near Threatened
LC: Least Concern
DD: Data Deficient

Details

Visit the website http://zoology.especies.cn/ for more details.

Value

object

Author(s)

Liuyong Ding [email protected]

Ke Yang [email protected]

References

http://zoology.especies.cn/

http://www.fungalinfo.net

http://www.iplant.cn/rep/protlist

http://www.mee.gov.cn

Examples

## Not run: 
#query assessment status via Chinese Names or Scientific Names
get_redlist_china(query = "Anguilla", option = "Scientific Names")
get_redlist_china(query = "Anguilla nebulosa", option = "Scientific Names")

#creates an HTML widget to display rectangular data
get_redlist_china(group = "Inland Fishes", viewDT = TRUE)

## End(Not run)
## Not run: 
#query assessment status via Chinese Names or Scientific Names
get_redlist_china(query = "Anguilla", option = "Scientific Names")
get_redlist_china(query = "Anguilla nebulosa", option = "Scientific Names")

#creates an HTML widget to display rectangular data
get_redlist_china(group = "Inland Fishes", viewDT = TRUE)

## End(Not run)

Download the top20 species for Catalogue of Life China checklist

Description

Download the most visited top20 species from http://sp2000.org.cnfor more details.

Usage

get_top20()
get_top20()

Details

Visit the website http://sp2000.org.cn for more details.

Value

top20 species

Author(s)

Liuyong Ding

Examples

## Not run: 
get_top20()

## End(Not run)
## Not run: 
get_top20()

## End(Not run)

Catalogue of Life list(s) convert data frame

Description

Checklist lists convert data frame.

Usage

list_df(x, db = c("colchina", "colglobal"))
list_df(x, db = c("colchina", "colglobal"))

Arguments

`x`	`list` Results returned by the function `search_checklist` and `get_col_global`.
`db`	`character` db = c("colchina","colglobal")

Format

A data frame with 19 variables:

ScientificName: The scientific name (the accepted name) includes the name and the date of the name
Synonyms: Synonyms name, Latin
ChineseName: Chinese name
CommonNames: Common name
Kingdom: Kingdom at taxonTree
Phylum: Phylum at taxonTree
Class: Class at taxonTree
Order: Order at taxonTree
Family: Family at taxonTree
Genus: Genus at taxonTree
Species: Species at taxonTree
Infraspecies: Infraspecies at taxonTree
Distribution: Distribution of species or infraspecies
Name: Full name of reviewer in English or Chinese
Email: Organization of the reviewer in English or Chinese
Address: Email address of the reviewer
Institution: Address of the reviewer in English or Chinese
References: References
Download: Download date

Author(s)

Liuyong Ding [email protected]

Source

Visit the website http://sp2000.org.cn/api/document for more details

Examples

## Not run: 
##Set your key
set_search_key <- "your apiKey"

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id, name = "familyID")

#Download detailed lists via species or infraspecies ID
query <- taxonid[["3851c5311bed46c19529cb155d37aa9b"]][["data"]][["namecode"]]
x1 <- search_checklist(query = query)
str(x1)
x1 <- list_df(x1,db = "colchina")

#Get Catalogue of Life Global checklist via species name
x2 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                               "Anguilla bicolor","Anguilla nebulosa",
                               "Anguilla luzonensis"),
                               option = "name")
str(x2)
x2 <- list_df(x2,db = "colglobal")

## End(Not run)
## Not run: 
##Set your key
set_search_key <- "your apiKey"

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id, name = "familyID")

#Download detailed lists via species or infraspecies ID
query <- taxonid[["3851c5311bed46c19529cb155d37aa9b"]][["data"]][["namecode"]]
x1 <- search_checklist(query = query)
str(x1)
x1 <- list_df(x1,db = "colchina")

#Get Catalogue of Life Global checklist via species name
x2 <- get_col_global(query = c("Anguilla marmorata","Anguilla japonica",
                               "Anguilla bicolor","Anguilla nebulosa",
                               "Anguilla luzonensis"),
                               option = "name")
str(x2)
x2 <- list_df(x2,db = "colglobal")

## End(Not run)

Opening the Catalogue of Life China checklist web pages with query

Description

Query with the accceptedName,scientificName,chineseName and commonName, returning the web pages that meets the criteria.

Usage

open_url(query = NULL, name = "accceptedName", language = "en")
open_url(query = NULL, name = "accceptedName", language = "en")

Arguments

`query`	`string` the accceptedName,scientificName,chineseName or commonName.
`name`	`string` name = c("accceptedName","scientificName","chineseName","commonName"),the default value is "accceptedName".
`language`	`string` currently only two languages are supported: Chinese and English,language=c("en","zh"), the default value is "en".

Details

Visit the website http://sp2000.org.cn/pageservices/document for more details.

Author(s)

Liuyong Ding

Liuyong Ding [email protected]

Examples


open_url(query = "Anguilla marmorata",name = "scientificName",language = 'en')
open_url(query = "Anguilla marmorata",name = "scientificName",language = 'zh')

open_url(query = "Anguilla marmorata",name = "scientificName",language = 'en')
open_url(query = "Anguilla marmorata",name = "scientificName",language = 'zh')

Search Catalogue of Life China checklist

Description

Get checklist via species or infraspecies ID.

Usage

search_checklist(query = NULL, mc.cores = 2)
search_checklist(query = NULL, mc.cores = 2)

Arguments

`query`	`string` One or more queries, see `search_family_id` and `search_taxon_id` for more details.
`mc.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized from environment variable MC_CORES if set. Must be at least one, and parallelization requires at least two cores,see `mclapply` for details.

Details

Visit the website http://sp2000.org.cn/api/document for more details.

Value

Catalogue of Life China list(s)

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id,name = "familyID")

#Download detailed lists via species or infraspecies ID
query <- taxonid[["3851c5311bed46c19529cb155d37aa9b"]][["data"]][["namecode"]]
x <- search_checklist(query = query)
str(x)

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id,name = "familyID")

#Download detailed lists via species or infraspecies ID
query <- taxonid[["3851c5311bed46c19529cb155d37aa9b"]][["data"]][["namecode"]]
x <- search_checklist(query = query)
str(x)

## End(Not run)

Search family IDs

Description

Search family IDs via family name, supports Latin and Chinese names.

Usage

search_family_id(query = NULL, start = 1, limit = 20, mc.cores = 2)
search_family_id(query = NULL, start = 1, limit = 20, mc.cores = 2)

Arguments

`query`	`character` One and more queries,support Family name, or part of family name, supports Latin and Chinese names.
`start`	`integer` Record number to start at. If omitted, the results are returned from the first record (start=1). Use in combination with limit to page through results. Note that we do the paging internally for you, but you can manually set the start parameter.
`limit`	`integer` Number of records to return, the default value is 20.
`mc.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized from environment variable MC_CORES if set. Must be at least one, and parallelization requires at least two cores,see `mclapply` for details.

Details

Visit the website http://sp2000.org.cn/api/document for more details

Value

dataframe

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

## End(Not run)

Search taxon IDs

Description

Search taxon IDs via familyID ,scientificName and commonName.

Usage

search_taxon_id(
  query = NULL,
  name = "scientificName",
  start = 1,
  limit = 20,
  mc.cores = 2
)
search_taxon_id(
  query = NULL,
  name = "scientificName",
  start = 1,
  limit = 20,
  mc.cores = 2
)

Arguments

`query`	`string` familyID ,scientificName or commonName.
`name`	`character` name = c("familyID","scientificName","commonName"),the default value is "scientificName".
`start`	`intenger` Record number to start at. If omitted, the results are returned from the first record (start=1). Use in combination with limit to page through results. Note that we do the paging internally for you, but you can manually set the start parameter.
`limit`	`intenger` Number of records to return. This is passed across all sources,when you first query, set the limit to something smallish so that you can get a result quickly, then do more as needed.
`mc.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized from environment variable MC_CORES if set. Must be at least one, and parallelization requires at least two cores,see `mclapply` for details.

Format

query:

taxonIDs: an array of species' ids
familyID: family ID, unique value
scientificName: the scientific name, or part of the scientific name, supports Latin names and Chinese
commonName: common name, or part of common name

Details

Visit the website http://sp2000.org.cn/api/document for more details

Value

dataframe

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id,name = "familyID")


## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "sp2000")

##Search family IDs via family name
familyid <- search_family_id(query = "Anguillidae")

##Search taxon IDs via familyID
taxonid <- search_taxon_id(query = familyid$Anguillidae$data$record_id,name = "familyID")


## End(Not run)

Apply for the apiKey variable to be used by all search_* functions and zoology_* functions, register for http://sp2000.org.cn/api/document and use an API key. This function allows users to set this key. Note: The daily API visits of ordinary users are 2000, If you want to apply for increasing the daily API request limit, please fill in the application form http://col.especies.cn/doc/API.docx and send an email to [email protected] entitled "Application for increasing API Request Times".

Usage

set_search_key(key, db = "sp2000")
set_search_key(key, db = "sp2000")

Arguments

`key`	`string` Value to set apiKey to (i.e. your API key).
`db`	`string` Set up the database API, db = c("sp2000","zoology").

Value

A logical of length one, TRUE is the value was set FALSE if not. value is returned inside invisible(), i.e. it is not printed to screen when the function is called.

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
#Set the apiKey variable to be used by all search_* functions
set_search_key("your apiKey",db = "sp2000")

#Set the apiKey variable to be used by all zoology_* functions
set_search_key("your apiKey",db = "zoology")


## End(Not run)
## Not run: 
#Set the apiKey variable to be used by all search_* functions
set_search_key("your apiKey",db = "sp2000")

#Set the apiKey variable to be used by all zoology_* functions
set_search_key("your apiKey",db = "zoology")


## End(Not run)

Query details of species in China Animal Scientific Database

Description

Query the database name and return a collection of names for all databases.

Usage

zoology_dbase_name()
zoology_dbase_name()

Format

China Animal Scientific Database

1: Chinese zoology database
2: China Animal Map Database
3: China Economic Animal Database
4: Chinese Bird Database
5: Chinese Mammal Database
6: China Butterfly Database
7: Chinese Bee Database
8: China Inland Water Fish Database
9: Chinese Amphibian Database
10: Chinese Reptile database
...: allow additional more databases to be used

Details

Visit the website http://zoology.especies.cn for more details.

Value

A collection of names for all China animal scientific databases

Author(s)

Liuyong Ding [email protected]

Ke Yang [email protected]

References

http://zoology.especies.cn

Examples

## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

#Query China Animal Scientific Database lists
zoology_dbase_name()

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

#Query China Animal Scientific Database lists
zoology_dbase_name()

## End(Not run)

Query details of species in China Animal Scientific Database

Description

Query the description information based on the species name, database name, and description type.

Query the description type information based on the species name and database name.

Usage

zoology_description(query, dbname, destype)

zoology_description_type(query, dbname)
zoology_description(query, dbname, destype)

zoology_description_type(query, dbname)

Arguments

`query`	`string` The string to query for scientific names.
`dbname`	`integer` There is one required parameter, a single numeric that indicates which China animal scientific database to use. Details in `zoology_dbase_name` for the list of available databases.
`destype`	`integer` There is one required parameter, a single numeric that indicates which description type information to use. Details in `zoology_description` for the list of available description type information based on the species name and database name.

Details

Visit the website http://zoology.especies.cn for more details.

Value

details of species in China Animal Scientific Database

description type information

Author(s)

Liuyong Ding [email protected]

Examples

## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

##Query details of species in Chinese Bird Database
zoology_description(query = "Aix galericulata",dbname = 4,destype = 209)

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

##Query description type information of Chinese Bird Database
zoology_description_type(query = "Aix galericulata",dbname = 4)

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

##Query details of species in Chinese Bird Database
zoology_description(query = "Aix galericulata",dbname = 4,destype = 209)

## End(Not run)
## Not run: 
##Set your key
set_search_key("your apiKey",db = "zoology")

##Query description type information of Chinese Bird Database
zoology_description_type(query = "Aix galericulata",dbname = 4)

## End(Not run)

Package 'SP2000'

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