rgbif
now has the ability to clean data retrieved from GBIF based on GBIF issues. These issues are returned in data retrieved from GBIF, e.g., through the occ_search()
function. Inspired by magrittr
, we've setup a workflow for cleaning data based on using the operator %>%
. You don't have to use it, but as we show below, it can make the process quite easy.
Note that you can also query based on issues, e.g., occ_search(taxonKey=1, issue='DEPTH_UNLIKELY')
. However, we imagine it's more likely that you want to search for occurrences based on a taxonomic name, or geographic area, not based on issues, so it makes sense to pull data down, then clean as needed using the below workflow with occ_issues()
.
Note that occ_issues()
only affects the data element in the gbif class that is returned from a call to occ_search()
. Maybe in a future version we will remove the associated records from the hierarchy and media elements as they are remove from the data element.
occ_issues()
also works with data from occ_download()
.
Install from CRAN
install.packages("rgbif")
Or install the development version from GitHub
devtools::install_github("ropensci/rgbif")
Load rgbif
library('rgbif')
Get taxon key for Helianthus annuus
(key <- name_suggest(q='Helianthus annuus', rank='species')$key[1])
#> [1] 9206251
Then pass to occ_search()
(res <- occ_search(taxonKey=key, limit=100))
#> Records found [45844]
#> Records returned [100]
#> No. unique hierarchies [1]
#> No. media records [84]
#> No. facets [0]
#> Args [limit=100, offset=0, taxonKey=9206251, fields=all]
#> # A tibble: 100 x 103
#> key scientificName decimalLatitude decimalLongitude issues datasetKey
#> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 1990… Helianthus an… 52.6 10.1 cdrou… 6ac3f774-…
#> 2 2235… Helianthus an… 51.2 4.45 "" 7f5e4129-…
#> 3 1990… Helianthus an… 26.2 -98.2 cdrou… 50c9509d-…
#> 4 2247… Helianthus an… 58.4 11.9 cdrou… 38b4c89f-…
#> 5 1993… Helianthus an… 34.0 -117. cdrou… 50c9509d-…
#> 6 1986… Helianthus an… 27.7 -97.3 cdrou… 50c9509d-…
#> 7 1993… Helianthus an… 33.4 -118. cdrou… 50c9509d-…
#> 8 1990… Helianthus an… 53.9 10.9 cdrou… 6ac3f774-…
#> 9 1986… Helianthus an… 33.8 -118. cdrou… 50c9509d-…
#> 10 2247… Helianthus an… 55.7 14.2 gass84 38b4c89f-…
#> # … with 90 more rows, and 97 more variables: publishingOrgKey <chr>,
#> # networkKeys <chr>, installationKey <chr>, publishingCountry <chr>,
#> # protocol <chr>, lastCrawled <chr>, lastParsed <chr>, crawlId <int>,
#> # extensions <chr>, basisOfRecord <chr>, taxonKey <int>,
#> # kingdomKey <int>, phylumKey <int>, classKey <int>, orderKey <int>,
#> # familyKey <int>, genusKey <int>, speciesKey <int>,
#> # acceptedTaxonKey <int>, acceptedScientificName <chr>, kingdom <chr>,
#> # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> # genericName <chr>, specificEpithet <chr>, taxonRank <chr>,
#> # taxonomicStatus <chr>, coordinateUncertaintyInMeters <dbl>,
#> # year <int>, month <int>, day <int>, eventDate <chr>,
#> # lastInterpreted <chr>, license <chr>, identifiers <chr>, facts <chr>,
#> # relations <chr>, geodeticDatum <chr>, class <chr>, countryCode <chr>,
#> # country <chr>, catalogNumber <chr>, recordedBy <chr>,
#> # institutionCode <chr>, locality <chr>, gbifID <chr>,
#> # collectionCode <chr>, name <chr>, individualCount <int>,
#> # continent <chr>, stateProvince <chr>, references <chr>,
#> # rightsHolder <chr>, identifier <chr>, informationWithheld <chr>,
#> # nomenclaturalCode <chr>, municipality <chr>, datasetName <chr>,
#> # identificationVerificationStatus <chr>, language <chr>,
#> # occurrenceID <chr>, type <chr>, taxonID <chr>, vernacularName <chr>,
#> # datasetID <chr>, samplingProtocol <chr>, accessRights <chr>,
#> # reproductiveCondition <chr>, dateIdentified <chr>, modified <chr>,
#> # http...unknown.org.nick <chr>, verbatimEventDate <chr>,
#> # verbatimLocality <chr>, http...unknown.org.occurrenceDetails <chr>,
#> # rights <chr>, eventTime <chr>, identificationID <chr>, county <chr>,
#> # occurrenceStatus <chr>, taxonConceptID <chr>, endDayOfYear <chr>,
#> # startDayOfYear <chr>, higherClassification <chr>,
#> # occurrenceRemarks <chr>, elevation <dbl>, recordNumber <chr>,
#> # georeferencedBy <chr>, associatedTaxa <chr>,
#> # http...unknown.org.recordId <chr>, otherCatalogNumbers <chr>,
#> # collectionID <chr>, georeferenceSources <chr>, habitat <chr>,
#> # identificationRemarks <chr>
The dataset gbifissues
can be retrieved using the function gbif_issues()
. The dataset's first column code
is a code that is used by default in the results from occ_search()
, while the second column issue
is the full issue name given by GBIF. The third column is a full description of the issue.
head(gbif_issues())
#> code issue
#> 1 bri BASIS_OF_RECORD_INVALID
#> 2 ccm CONTINENT_COUNTRY_MISMATCH
#> 3 cdc CONTINENT_DERIVED_FROM_COORDINATES
#> 4 conti CONTINENT_INVALID
#> 5 cdiv COORDINATE_INVALID
#> 6 cdout COORDINATE_OUT_OF_RANGE
#> description
#> 1 The given basis of record is impossible to interpret or seriously different from the recommended vocabulary.
#> 2 The interpreted continent and country do not match up.
#> 3 The interpreted continent is based on the coordinates, not the verbatim string information.
#> 4 Uninterpretable continent values found.
#> 5 Coordinate value given in some form but GBIF is unable to interpret it.
#> 6 Coordinate has invalid lat/lon values out of their decimal max range.
#> type
#> 1 occurrence
#> 2 occurrence
#> 3 occurrence
#> 4 occurrence
#> 5 occurrence
#> 6 occurrence
You can query to get certain issues
gbif_issues()[ gbif_issues()$code %in% c('cdround','cudc','gass84','txmathi'), ]
#> code issue
#> 10 cdround COORDINATE_ROUNDED
#> 12 cudc COUNTRY_DERIVED_FROM_COORDINATES
#> 23 gass84 GEODETIC_DATUM_ASSUMED_WGS84
#> 39 txmathi TAXON_MATCH_HIGHERRANK
#> description
#> 10 Original coordinate modified by rounding to 5 decimals.
#> 12 The interpreted country is based on the coordinates, not the verbatim string information.
#> 23 Indicating that the interpreted coordinates assume they are based on WGS84 datum as the datum was either not indicated or interpretable.
#> 39 Matching to the taxonomic backbone can only be done on a higher rank and not the scientific name.
#> type
#> 10 occurrence
#> 12 occurrence
#> 23 occurrence
#> 39 occurrence
The code cdround
represents the GBIF issue COORDINATE_ROUNDED
, which means that
Original coordinate modified by rounding to 5 decimals.
The content for this information comes from http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/OccurrenceIssue.html.
Now that we know a bit about GBIF issues, you can parse your data based on issues. Using the data generated above, and using the function %>%
imported from magrittr
, we can get only data with the issue gass84
, or GEODETIC_DATUM_ASSUMED_WGS84
(Note how the records returned goes down to 98 instead of the initial 100).
res %>%
occ_issues(gass84)
#> Records found [45844]
#> Records returned [99]
#> No. unique hierarchies [1]
#> No. media records [84]
#> No. facets [0]
#> Args [limit=100, offset=0, taxonKey=9206251, fields=all]
#> # A tibble: 99 x 103
#> key scientificName decimalLatitude decimalLongitude issues datasetKey
#> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 1990… Helianthus an… 52.6 10.1 cdrou… 6ac3f774-…
#> 2 1990… Helianthus an… 26.2 -98.2 cdrou… 50c9509d-…
#> 3 2247… Helianthus an… 58.4 11.9 cdrou… 38b4c89f-…
#> 4 1993… Helianthus an… 34.0 -117. cdrou… 50c9509d-…
#> 5 1986… Helianthus an… 27.7 -97.3 cdrou… 50c9509d-…
#> 6 1993… Helianthus an… 33.4 -118. cdrou… 50c9509d-…
#> 7 1990… Helianthus an… 53.9 10.9 cdrou… 6ac3f774-…
#> 8 1986… Helianthus an… 33.8 -118. cdrou… 50c9509d-…
#> 9 2247… Helianthus an… 55.7 14.2 gass84 38b4c89f-…
#> 10 2236… Helianthus an… 26.2 -98.2 cdrou… 50c9509d-…
#> # … with 89 more rows, and 97 more variables: publishingOrgKey <chr>,
#> # networkKeys <chr>, installationKey <chr>, publishingCountry <chr>,
#> # protocol <chr>, lastCrawled <chr>, lastParsed <chr>, crawlId <int>,
#> # extensions <chr>, basisOfRecord <chr>, taxonKey <int>,
#> # kingdomKey <int>, phylumKey <int>, classKey <int>, orderKey <int>,
#> # familyKey <int>, genusKey <int>, speciesKey <int>,
#> # acceptedTaxonKey <int>, acceptedScientificName <chr>, kingdom <chr>,
#> # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> # genericName <chr>, specificEpithet <chr>, taxonRank <chr>,
#> # taxonomicStatus <chr>, coordinateUncertaintyInMeters <dbl>,
#> # year <int>, month <int>, day <int>, eventDate <chr>,
#> # lastInterpreted <chr>, license <chr>, identifiers <chr>, facts <chr>,
#> # relations <chr>, geodeticDatum <chr>, class <chr>, countryCode <chr>,
#> # country <chr>, catalogNumber <chr>, recordedBy <chr>,
#> # institutionCode <chr>, locality <chr>, gbifID <chr>,
#> # collectionCode <chr>, name <chr>, individualCount <int>,
#> # continent <chr>, stateProvince <chr>, references <chr>,
#> # rightsHolder <chr>, identifier <chr>, informationWithheld <chr>,
#> # nomenclaturalCode <chr>, municipality <chr>, datasetName <chr>,
#> # identificationVerificationStatus <chr>, language <chr>,
#> # occurrenceID <chr>, type <chr>, taxonID <chr>, vernacularName <chr>,
#> # datasetID <chr>, samplingProtocol <chr>, accessRights <chr>,
#> # reproductiveCondition <chr>, dateIdentified <chr>, modified <chr>,
#> # http...unknown.org.nick <chr>, verbatimEventDate <chr>,
#> # verbatimLocality <chr>, http...unknown.org.occurrenceDetails <chr>,
#> # rights <chr>, eventTime <chr>, identificationID <chr>, county <chr>,
#> # occurrenceStatus <chr>, taxonConceptID <chr>, endDayOfYear <chr>,
#> # startDayOfYear <chr>, higherClassification <chr>,
#> # occurrenceRemarks <chr>, elevation <dbl>, recordNumber <chr>,
#> # georeferencedBy <chr>, associatedTaxa <chr>,
#> # http...unknown.org.recordId <chr>, otherCatalogNumbers <chr>,
#> # collectionID <chr>, georeferenceSources <chr>, habitat <chr>,
#> # identificationRemarks <chr>
Note also that we've set up occ_issues()
so that you can pass in issue names without having to quote them, thereby speeding up data cleaning.
Next, we can remove data with certain issues just as easily by using a -
sign in front of the variable, like this, removing data with issues depunl
and mdatunl
.
res %>%
occ_issues(-depunl, -mdatunl)
#> Records found [45844]
#> Records returned [100]
#> No. unique hierarchies [1]
#> No. media records [84]
#> No. facets [0]
#> Args [limit=100, offset=0, taxonKey=9206251, fields=all]
#> # A tibble: 100 x 103
#> key scientificName decimalLatitude decimalLongitude issues datasetKey
#> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 1990… Helianthus an… 52.6 10.1 cdrou… 6ac3f774-…
#> 2 2235… Helianthus an… 51.2 4.45 "" 7f5e4129-…
#> 3 1990… Helianthus an… 26.2 -98.2 cdrou… 50c9509d-…
#> 4 2247… Helianthus an… 58.4 11.9 cdrou… 38b4c89f-…
#> 5 1993… Helianthus an… 34.0 -117. cdrou… 50c9509d-…
#> 6 1986… Helianthus an… 27.7 -97.3 cdrou… 50c9509d-…
#> 7 1993… Helianthus an… 33.4 -118. cdrou… 50c9509d-…
#> 8 1990… Helianthus an… 53.9 10.9 cdrou… 6ac3f774-…
#> 9 1986… Helianthus an… 33.8 -118. cdrou… 50c9509d-…
#> 10 2247… Helianthus an… 55.7 14.2 gass84 38b4c89f-…
#> # … with 90 more rows, and 97 more variables: publishingOrgKey <chr>,
#> # networkKeys <chr>, installationKey <chr>, publishingCountry <chr>,
#> # protocol <chr>, lastCrawled <chr>, lastParsed <chr>, crawlId <int>,
#> # extensions <chr>, basisOfRecord <chr>, taxonKey <int>,
#> # kingdomKey <int>, phylumKey <int>, classKey <int>, orderKey <int>,
#> # familyKey <int>, genusKey <int>, speciesKey <int>,
#> # acceptedTaxonKey <int>, acceptedScientificName <chr>, kingdom <chr>,
#> # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> # genericName <chr>, specificEpithet <chr>, taxonRank <chr>,
#> # taxonomicStatus <chr>, coordinateUncertaintyInMeters <dbl>,
#> # year <int>, month <int>, day <int>, eventDate <chr>,
#> # lastInterpreted <chr>, license <chr>, identifiers <chr>, facts <chr>,
#> # relations <chr>, geodeticDatum <chr>, class <chr>, countryCode <chr>,
#> # country <chr>, catalogNumber <chr>, recordedBy <chr>,
#> # institutionCode <chr>, locality <chr>, gbifID <chr>,
#> # collectionCode <chr>, name <chr>, individualCount <int>,
#> # continent <chr>, stateProvince <chr>, references <chr>,
#> # rightsHolder <chr>, identifier <chr>, informationWithheld <chr>,
#> # nomenclaturalCode <chr>, municipality <chr>, datasetName <chr>,
#> # identificationVerificationStatus <chr>, language <chr>,
#> # occurrenceID <chr>, type <chr>, taxonID <chr>, vernacularName <chr>,
#> # datasetID <chr>, samplingProtocol <chr>, accessRights <chr>,
#> # reproductiveCondition <chr>, dateIdentified <chr>, modified <chr>,
#> # http...unknown.org.nick <chr>, verbatimEventDate <chr>,
#> # verbatimLocality <chr>, http...unknown.org.occurrenceDetails <chr>,
#> # rights <chr>, eventTime <chr>, identificationID <chr>, county <chr>,
#> # occurrenceStatus <chr>, taxonConceptID <chr>, endDayOfYear <chr>,
#> # startDayOfYear <chr>, higherClassification <chr>,
#> # occurrenceRemarks <chr>, elevation <dbl>, recordNumber <chr>,
#> # georeferencedBy <chr>, associatedTaxa <chr>,
#> # http...unknown.org.recordId <chr>, otherCatalogNumbers <chr>,
#> # collectionID <chr>, georeferenceSources <chr>, habitat <chr>,
#> # identificationRemarks <chr>
Another thing we can do with occ_issues()
is go from issue codes to full issue names in case you want those in your dataset (here, showing only a few columns to see the data better for this demo):
out <- res %>% occ_issues(mutate = "expand")
head(out$data[,c(1,5)])
#> # A tibble: 6 x 2
#> key issues
#> <chr> <chr>
#> 1 1990684609 COORDINATE_ROUNDED,GEODETIC_DATUM_ASSUMED_WGS84
#> 2 2235291308 ""
#> 3 1990481993 COORDINATE_ROUNDED,GEODETIC_DATUM_ASSUMED_WGS84
#> 4 2247028617 COORDINATE_ROUNDED,GEODETIC_DATUM_ASSUMED_WGS84
#> 5 1993715633 COORDINATE_ROUNDED,GEODETIC_DATUM_ASSUMED_WGS84
#> 6 1986613930 COORDINATE_ROUNDED,GEODETIC_DATUM_ASSUMED_WGS84
Sometimes you may want to have each type of issue as a separate column.
Split out each issue type into a separate column, with number of columns equal to number of issue types
out <- res %>% occ_issues(mutate = "split")
head(out$data[,c(1,5:10)])
#> # A tibble: 6 x 7
#> name cdround gass84 gdativ scientificName datasetKey publishingOrgKey
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Helia… y y n Helianthus ann… 6ac3f774-d… bb646dff-a905-4…
#> 2 Helia… n n n Helianthus ann… 7f5e4129-0… 4d3ceea8-5699-4…
#> 3 Helia… y y n Helianthus ann… 50c9509d-2… 28eb1a3f-1c15-4…
#> 4 Helia… y y n Helianthus ann… 38b4c89f-5… b8323864-602a-4…
#> 5 Helia… y y n Helianthus ann… 50c9509d-2… 28eb1a3f-1c15-4…
#> 6 Helia… y y n Helianthus ann… 50c9509d-2… 28eb1a3f-1c15-4…
Or you can expand each issue type into its full name, and split each issue into a separate column.
out <- res %>% occ_issues(mutate = "split_expand")
head(out$data[,c(1,5:10)])
#> # A tibble: 6 x 7
#> name COORDINATE_ROUN… GEODETIC_DATUM_… GEODETIC_DATUM_… scientificName
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Heli… y y n Helianthus an…
#> 2 Heli… n n n Helianthus an…
#> 3 Heli… y y n Helianthus an…
#> 4 Heli… y y n Helianthus an…
#> 5 Heli… y y n Helianthus an…
#> 6 Heli… y y n Helianthus an…
#> # … with 2 more variables: datasetKey <chr>, publishingOrgKey <chr>
We hope this helps users get just the data they want, and nothing more. Let us know if you have feedback on data cleaning functionality in rgbif
at info@ropensci.org or at https://github.com/ropensci/rgbif/issues.