This rnsii package programatically download Chinese biodiversity data from the National Specimen Information Infrastructure http://www.nsii.org.cn .
Installation using R package devtools:
if (!requireNamespace(c("devtools","tibble"), quietly = TRUE))
install.packages("devtools","tibble")
devtools::install_github("Otoliths/rnsii",build_vignettes = TRUE)
library("rnsii")
result1 <- get_nsii(query = "Artemisia argyi",offset = 0)
# Download date: 2021-03-25
# No encoding supplied: defaulting to UTF-8.
# Query successfully: Artemisia argyi(1796)
str(result1)
# List of 5
# $ from : chr "国家植物标本资源库"
# $ total : int 1796
# $ offset: int 0
# $ limit : int 30
# $ data :'data.frame': 30 obs. of 13 variables:
# ..$ collectionID : chr [1:30] "bca470dc" "bca47178" "bca47214" "bca472b0" ...
# ..$ institutionCode: chr [1:30] "WUK" "WUK" "WUK" "WUK" ...
# ..$ collectionCode : chr [1:30] "0357558" "0371743" "0365274" "0356022" ...
# ..$ canonicalName : chr [1:30] "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" ...
# ..$ formattedName : chr [1:30] "<em>Artemisia argyi</em> <em></em> <em></em>" "<em>Artemisia argyi</em> <em></em> <em></em>" "<em>Artemisia argyi</em> <em></em> <em></em>" "<em>Artemisia argyi</em> <em></em> <em></em>" ...
# ..$ chineseName : chr [1:30] "艾" "艾" "艾" "艾" ...
# ..$ recordNumber : chr [1:30] "11193" "10505" "18245" "8733" ...
# ..$ year : chr [1:30] "1959" "1959" "1978" "1959" ...
# ..$ recordedBy : chr [1:30] "李培元" "张志英" "张志英" "李培元" ...
# ..$ country : chr [1:30] "中国" "中国" "中国" "中国" ...
# ..$ stateProvince : chr [1:30] "湖北省" "甘肃省" "陕西省" "陕西省" ...
# ..$ withPhoto : chr [1:30] "0" "0" "0" "0" ...
# ..$ isType : chr [1:30] "0" "0" "0" "0" ..
tibble::tibble(result1$data)
# # A tibble: 30 x 13
# collectionID institutionCode collectionCode canonicalName formattedName chineseName recordNumber
# <chr> <chr> <chr> <chr> <chr> <chr> <chr>
# 1 bca470dc WUK 0357558 Artemisia arg… <em>Artemisi… 艾 11193
# 2 bca47178 WUK 0371743 Artemisia arg… <em>Artemisi… 艾 10505
# 3 bca47214 WUK 0365274 Artemisia arg… <em>Artemisi… 艾 18245
# 4 bca472b0 WUK 0356022 Artemisia arg… <em>Artemisi… 艾 8733
# 5 bca4734b WUK 0405413 Artemisia arg… <em>Artemisi… 艾 3069
# 6 bca473e5 WUK 0354634 Artemisia arg… <em>Artemisi… 艾 7229
# 7 bdaf9f8f WUK 0374515 Artemisia arg… <em>Artemisi… 艾 13693
# 8 bdafa02b WUK 0360427 Artemisia arg… <em>Artemisi… 艾 10905
# 9 bdafa0c7 WUK 0288094 Artemisia arg… <em>Artemisi… 艾 2089
# 10 bdafa164 WUK 0282248 Artemisia arg… <em>Artemisi… 艾 27
# # … with 20 more rows, and 6 more variables: year <chr>, recordedBy <chr>, country <chr>,
# # stateProvince <chr>, withPhoto <chr>, isType <chr>
result2 <- get_occ(query = "Artemisia argyi")
# Download date: 2021-03-03
# Query successfully: Artemisia argyi
# Include latitude and longitude: Artemisia argyi
str(result2)
# List of 10
# $ Title : chr "Artemisia argyi"
# $ Description: chr "多年生草本或略成半灌木状，植株有浓烈香气。主根明显，略粗长，直径达1.5厘米，侧根多；常有横卧地下根状茎及营养枝。"| __truncated__
# $ QueryName : chr "Artemisia argyi"
# $ LatinName : chr "Artemisia argyi"
# $ CommonName : chr "艾"
# $ Images :'data.frame': 1 obs. of 5 variables:
# ..$ title : chr "Artemisia argyi"
# ..$ description: chr ""
# ..$ type : chr "image"
# ..$ source : chr "http://www.nsii.org.cn/eol/eolmedia/13256627.jpg"
# ..$ url : chr "http://www.nsii.org.cn"
# $ Specimens :'data.frame': 921 obs. of 9 variables:
# ..$ barcode : chr [1:921] "0021954" "0021953" "0021952" "0000681" ...
# ..$ sname : chr [1:921] "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" ...
# ..$ commonName : chr [1:921] "艾" "艾" "艾" "艾" ...
# ..$ latitude : num [1:921] 29.8 31.6 30.2 31.3 31.3 31.3 33.8 34.1 37.4 37.4 ...
# ..$ longitude : num [1:921] 110 111 109 109 109 ...
# ..$ recordedby : chr [1:921] "李洪钧" "鄂神农架植考队" "黄仁煌" "方明渊" ...
# ..$ recordnumber: chr [1:921] "5984" "21740" "3389" "23960" ...
# ..$ locality : chr [1:921] "中国湖北鹤峰县" "中国湖北神农架林区" "中国湖北利川市" "中国重庆奉节县" ...
# ..$ year : chr [1:921] "1958" "1976" "1975" "1958" ...
# $ StatusCode : int 0
# $ Status : chr "ok"
# $ Message : chr ""
tibble::tibble(result2$Specimens)
# List of 10
# $ Title : chr "Artemisia argyi"
# $ Description: chr "多年生草本或略成半灌木状，植株有浓烈香气。主根明显，略粗长，直径达1.5厘米，侧根多；常有横卧地下根状茎及营养枝。"| __truncated__
# $ QueryName : chr "Artemisia argyi"
# $ LatinName : chr "Artemisia argyi"
# $ CommonName : chr "艾"
# $ Images :'data.frame': 1 obs. of 5 variables:
# ..$ title : chr "Artemisia argyi"
# ..$ description: chr ""
# ..$ type : chr "image"
# ..$ source : chr "http://www.nsii.org.cn/eol/eolmedia/13256627.jpg"
# ..$ url : chr "http://www.nsii.org.cn"
# $ Specimens :'data.frame': 921 obs. of 9 variables:
# ..$ barcode : chr [1:921] "0021954" "0021953" "0021952" "0000681" ...
# ..$ sname : chr [1:921] "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" ...
# ..$ commonName : chr [1:921] "艾" "艾" "艾" "艾" ...
# ..$ latitude : num [1:921] 29.8 31.6 30.2 31.3 31.3 31.3 33.8 34.1 37.4 37.4 ...
# ..$ longitude : num [1:921] 110 111 109 109 109 ...
# ..$ recordedby : chr [1:921] "李洪钧" "鄂神农架植考队" "黄仁煌" "方明渊" ...
# ..$ recordnumber: chr [1:921] "5984" "21740" "3389" "23960" ...
# ..$ locality : chr [1:921] "中国湖北鹤峰县" "中国湖北神农架林区" "中国湖北利川市" "中国重庆奉节县" ...
# ..$ year : chr [1:921] "1958" "1976" "1975" "1958" ...
# $ StatusCode : int 0
# $ Status : chr "ok"
# $ Message : chr ""
# # A tibble: 921 x 9
# barcode sname commonName latitude longitude recordedby recordnumber locality year
# <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr>
# 1 0021954 Artemisia argyi 艾 29.8 110. 李洪钧 5984 中国湖北鹤峰县 1958
# 2 0021953 Artemisia argyi 艾 31.6 111. 鄂神农架植考队 21740 中国湖北神农架林区 1976
# 3 0021952 Artemisia argyi 艾 30.2 109. 黄仁煌 3389 中国湖北利川市 1975
# 4 0000681 Artemisia argyi 艾 31.3 109. 方明渊 23960 中国重庆奉节县 1958
# 5 0000680 Artemisia argyi 艾 31.3 109 张泽荣 25990 中国重庆奉节县 1958
# 6 0000677 Artemisia argyi 艾 31.3 109. 方明渊 24868 中国重庆奉节县 1958
# 7 0000676 Artemisia argyi 艾 33.8 108. 张襄明 350 中国陕西周至县 1958
# 8 0000675 Artemisia argyi 艾 34.1 108. 张襄明 947 中国陕西眉县 1958
# 9 0000671 Artemisia argyi 艾 37.4 114 刘鑫源 914 中国河北赞皇县 1951
# 10 0000670 Artemisia argyi 艾 37.4 114 刘鑫源 1101 中国河北赞皇县 1951
# # … with 911 more rows
citation("rnsii")To cite package ‘rnsii’ in publications use:
Liuyong Ding (2021). rnsii: Interface to the National Specimen Information Infrastructure. R package version 0.1.0.
A BibTeX entry for LaTeX users is
@Manual{,
title = {rnsii: Interface to the National Specimen Information Infrastructure},
author = {Liuyong Ding},
year = {2021},
note = {R package version 0.1.0},
}Contributions to this package are welcome. The preferred method of contribution is through a GitHub pull request. Feel also free to contact us by creating an issue.