rnsii-vegnette.RmdThis 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")## Downloading GitHub repo Otoliths/rnsii@HEAD##
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checking for file ‘/private/var/folders/1x/5mjvgdgx0m754gnfv6_dyxqm0000gn/T/RtmpxF4fQH/remotesd87b1fdc7e19/Otoliths-rnsii-0c06217/DESCRIPTION’ ...
✓ checking for file ‘/private/var/folders/1x/5mjvgdgx0m754gnfv6_dyxqm0000gn/T/RtmpxF4fQH/remotesd87b1fdc7e19/Otoliths-rnsii-0c06217/DESCRIPTION’
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─ preparing ‘rnsii’:
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checking DESCRIPTION meta-information ...
✓ checking DESCRIPTION meta-information
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─ installing the package to process help pages
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─ saving partial Rd database (1.5s)
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─ checking for LF line-endings in source and make files and shell scripts
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─ checking for empty or unneeded directories
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─ building ‘rnsii_0.2.0.tar.gz’
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## ## Installing package into '/private/var/folders/1x/5mjvgdgx0m754gnfv6_dyxqm0000gn/T/Rtmpu9KCIz/temp_libpathd8025f44ce93'
## (as 'lib' is unspecified)
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
## <chr> <chr> <chr> <chr> <chr>
## 1 bca470dc WUK 0357558 Artemisia arg… <em>Artemisia arg…
## 2 bca47178 WUK 0371743 Artemisia arg… <em>Artemisia arg…
## 3 bca47214 WUK 0365274 Artemisia arg… <em>Artemisia arg…
## 4 bca472b0 WUK 0356022 Artemisia arg… <em>Artemisia arg…
## 5 bca4734b WUK 0405413 Artemisia arg… <em>Artemisia arg…
## 6 bca473e5 WUK 0354634 Artemisia arg… <em>Artemisia arg…
## 7 bdaf9f8f WUK 0374515 Artemisia arg… <em>Artemisia arg…
## 8 bdafa02b WUK 0360427 Artemisia arg… <em>Artemisia arg…
## 9 bdafa0c7 WUK 0288094 Artemisia arg… <em>Artemisia arg…
## 10 bdafa164 WUK 0282248 Artemisia arg… <em>Artemisia arg…
## # … with 20 more rows, and 8 more variables: chineseName <chr>,
## # recordNumber <chr>, year <chr>, recordedBy <chr>, country <chr>,
## # stateProvince <chr>, withPhoto <chr>, isType <chr>
result2 <- get_occ(query = "Artemisia argyi")## Download date: 2021-03-25
## 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': 286 obs. of 9 variables:
## ..$ barcode : chr [1:286] "0021954" "0021953" "0021952" "0000681" ...
## ..$ sname : chr [1:286] "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" "Artemisia argyi" ...
## ..$ commonName : chr [1:286] "艾" "艾" "艾" "艾" ...
## ..$ latitude : num [1:286] 29.8 31.6 30.2 31.3 31.3 31.3 33.8 34.1 37.4 37.4 ...
## ..$ longitude : num [1:286] 110 111 109 109 109 ...
## ..$ recordedby : chr [1:286] "李洪钧" "鄂神农架植考队" "黄仁煌" "方明渊" ...
## ..$ recordnumber: chr [1:286] "5984" "21740" "3389" "23960" ...
## ..$ locality : chr [1:286] "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 [1:286] "1958" "1976" "1975" "1958" ...
## $ StatusCode : int 0
## $ Status : chr "ok"
## $ Message : chr ""
citation("rnsii")##
## To cite package 'rnsii' in publications use:
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## Liuyong Ding (2021). rnsii: Interface to the National Specimen
## Information Infrastructure. R package version 0.2.0.
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## A BibTeX entry for LaTeX users is
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## @Manual{,
## title = {rnsii: Interface to the National Specimen Information Infrastructure},
## author = {Liuyong Ding},
## year = {2021},
## note = {R package version 0.2.0},
## }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.