finch

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finch parses Darwin Core simple and archive files

In the future, we may make it easy to create Darwin Core archive files as well.

Install

Stable version

install.packages("finch")

Development version, from GitHub

devtools::install_github("ropensci/finch")
library("finch")

Parse

To parse a simple darwin core file like

<?xml version="1.0" encoding="UTF-8"?>
<SimpleDarwinRecordSet
 xmlns="http://rs.tdwg.org/dwc/xsd/simpledarwincore/"
 xmlns:dc="http://purl.org/dc/terms/"
 xmlns:dwc="http://rs.tdwg.org/dwc/terms/"
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 xsi:schemaLocation="http://rs.tdwg.org/dwc/xsd/simpledarwincore/ ../../xsd/tdwg_dwc_simple.xsd">
 <SimpleDarwinRecord>
  <dwc:occurrenceID>urn:catalog:YPM:VP.057488</dwc:occurrenceID>
  <dc:type>PhysicalObject</dc:type>
  <dc:modified>2009-02-12T12:43:31</dc:modified>
  <dc:language>en</dc:language>
  <dwc:basisOfRecord>FossilSpecimen</dwc:basisOfRecord>
  <dwc:institutionCode>YPM</dwc:institutionCode>
  <dwc:collectionCode>VP</dwc:collectionCode>
  <dwc:catalogNumber>VP.057488</dwc:catalogNumber>
  <dwc:individualCount>1</dwc:individualCount>
  <dwc:locationID xsi:nil="true"/>
  <dwc:continent>North America</dwc:continent>
  <dwc:country>United States</dwc:country>
  <dwc:countryCode>US</dwc:countryCode>
  <dwc:stateProvince>Montana</dwc:stateProvince>
  <dwc:county>Garfield</dwc:county>
  <dwc:scientificName>Tyrannosourus rex</dwc:scientificName>
  <dwc:genus>Tyrannosourus</dwc:genus>
  <dwc:specificEpithet>rex</dwc:specificEpithet>
  <dwc:earliestPeriodOrHighestSystem>Creataceous</dwc:earliestPeriodOrHighestSystem>
  <dwc:latestPeriodOrHighestSystem>Creataceous</dwc:latestPeriodOrHighestSystem>
  <dwc:earliestEonOrHighestEonothem>Late Cretaceous</dwc:earliestEonOrHighestEonothem>
  <dwc:latestEonOrHighestEonothem>Late Cretaceous</dwc:latestEonOrHighestEonothem>
 </SimpleDarwinRecord>
</SimpleDarwinRecordSet>

This file is in this package as an example file, get the file, then simple()

file <- system.file("examples", "example_simple_fossil.xml", package = "finch")
out <- simple_read(file)

Index to meta, dc or dwc

out$dc
#> [[1]]
#> [[1]]$type
#> [1] "PhysicalObject"
#> 
#> 
#> [[2]]
#> [[2]]$modified
#> [1] "2009-02-12T12:43:31"
#> 
#> 
#> [[3]]
#> [[3]]$language
#> [1] "en"

Parse Darwin Core Archive

To parse a Darwin Core Archive like can be gotten from GBIF use dwca_read()

There’s an example Darwin Core Archive:

file <- system.file("examples", "0000154-150116162929234.zip", package = "finch")
(out <- dwca_read(file, read = TRUE))
#> <gbif dwca>
#>   Package ID: 6cfaaf9c-d518-4ca3-8dc5-f5aadddc0390
#>   No. data sources: 10
#>   No. datasets: 3
#>   Dataset occurrence.txt: [225 X 443]
#>   Dataset multimedia.txt: [15 X 1]
#>   Dataset verbatim.txt: [209 X 443]

List files in the archive

out$files
#> $xml_files
#> [1] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/meta.xml"    
#> [2] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/metadata.xml"
#> 
#> $txt_files
#> [1] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/citations.txt" 
#> [2] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/multimedia.txt"
#> [3] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/occurrence.txt"
#> [4] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/rights.txt"    
#> [5] "/Users/sckott/Library/Caches/R/finch/0000154-150116162929234/verbatim.txt"  
...

High level metadata for the whole archive

out$emlmeta
#> <eml packageId="6cfaaf9c-d518-4ca3-8dc5-f5aadddc0390" system="http://gbif.org" scope="system" xml:lang="en" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 http://rs.gbif.org/schema/eml-gbif-profile/1.0.2/eml.xsd">
#>   <dataset>
#>     <title>GBIF Occurrence Download 0000154-150116162929234</title>
#>     <creator>
#>       <individualName>
#>         <surName>GBIF Download Service</surName>
#>       </individualName>
#>     </creator>
#>     <metadataProvider>
#>       <individualName>
#>         <surName>GBIF Download Service</surName>
#>       </individualName>
#>     </metadataProvider>
#>     <associatedParty>
#>       <organizationName>OZCAM (Online Zoological Collections of Australian Museums) Provider</organizationName>
#>       <onlineUrl>http://www.ozcam.org.au/</onlineUrl>
#>       <role>CONTENT_PROVIDER</role>
#>     </associatedParty>
#>     <associatedParty>
#>       <individualName>
...

High level metadata for each data file, there’s many files, but we’ll just look at one

hm <- out$highmeta
head( hm$occurrence.txt )
#>   index                                        term delimitedBy
#> 1     0         http://rs.gbif.org/terms/1.0/gbifID        <NA>
#> 2     1           http://purl.org/dc/terms/abstract        <NA>
#> 3     2       http://purl.org/dc/terms/accessRights        <NA>
#> 4     3      http://purl.org/dc/terms/accrualMethod        <NA>
#> 5     4 http://purl.org/dc/terms/accrualPeriodicity        <NA>
#> 6     5      http://purl.org/dc/terms/accrualPolicy        <NA>

You can get the same metadata as above for each dataset that went into the tabular dataset downloaded

out$dataset_meta[[1]]

View one of the datasets, brief overview.

head( out$data[[1]][,c(1:5)] )
#>      gbifID abstract accessRights accrualMethod accrualPeriodicity
#> 1  50280003       NA                         NA                 NA
#> 2 477550574       NA                         NA                 NA
#> 3 239703844       NA                         NA                 NA
#> 4 239703843       NA                         NA                 NA
#> 5 239703833       NA                         NA                 NA
#> 6 477550692       NA                         NA                 NA

You can also give dwca() a local directory, or url that contains a Darwin Core Archive.

Meta

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