rOpenSci: The finch package

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finch parses Darwin Core simple and archive files

Docs: https://docs.ropensci.org/finch/

Install

Stable version

Development version, from GitHub

remotes::install_github("ropensci/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
#> additionalMetadata:
#>   metadata:
#>     gbif:
#>       citation:
#>         identifier: 0000154-150116162929234
#>         citation: GBIF Occurrence Download 0000154-150116162929234
#>       physical:
#>         objectName: []
#>         characterEncoding: UTF-8
#>         dataFormat:
#>           externallyDefinedFormat:
#>             formatName: Darwin Core Archive
#>         distribution:
#>           online:
#>             url:
#>               function: download
#>               url: http://api.gbif.org/v1/occurrence/download/request/0000154-150116162929234.zip
#> dataset:
#>   title: GBIF Occurrence Download 0000154-150116162929234
#>   creator:
...

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