The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

finch

Build Status Build status cran checks codecov cran version

finch parses Darwin Core simple and archive files

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

Install

Stable version

install.packages("finch")

Development version, from GitHub

remotes::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
#> 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

rofooter

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.