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updated vignettes
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sckott committed Oct 7, 2015
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153 changes: 78 additions & 75 deletions inst/vign/issues_vignette.md
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Original file line number Diff line number Diff line change
Expand Up @@ -55,24 +55,24 @@ Then pass to `occ_search()`

```r
(res <- occ_search(taxonKey=key, limit=100))
#> Records found [20650]
#> Records found [21517]
#> Records returned [100]
#> No. unique hierarchies [1]
#> No. media records [36]
#> No. media records [60]
#> Args [taxonKey=3119195, limit=100, offset=0, fields=all]
#> First 10 rows of data
#>
#> name key decimalLatitude decimalLongitude
#> 1 Helianthus annuus 1095851641 0.00000 0.00000
#> 2 Helianthus annuus 1088900309 33.95239 -117.32011
#> 3 Helianthus annuus 1088933055 25.66564 -100.30348
#> 4 Helianthus annuus 1088909392 24.72449 -99.54020
#> 5 Helianthus annuus 1088937716 25.81691 -100.05940
#> 6 Helianthus annuus 1088944416 26.20518 -98.26725
#> 7 Helianthus annuus 1090389390 59.96150 17.71060
#> 8 Helianthus annuus 1092889365 32.71840 -114.75603
#> 9 Helianthus annuus 1092889645 1.27617 103.79136
#> 10 Helianthus annuus 1098903927 29.17958 -102.99551
#> 3 Helianthus annuus 1135826959 NA NA
#> 4 Helianthus annuus 1135523136 33.96709 -117.99769
#> 5 Helianthus annuus 1088944416 26.20518 -98.26725
#> 6 Helianthus annuus 1092901911 30.22344 -97.95281
#> 7 Helianthus annuus 1098903927 29.17958 -102.99551
#> 8 Helianthus annuus 1135523412 33.96787 -118.00016
#> 9 Helianthus annuus 1092894334 34.16052 -119.03794
#> 10 Helianthus annuus 1092889365 32.71840 -114.75603
#> .. ... ... ... ...
#> Variables not shown: issues (chr), datasetKey (chr), publishingOrgKey
#> (chr), publishingCountry (chr), protocol (chr), lastCrawled (chr),
Expand All @@ -85,19 +85,20 @@ Then pass to `occ_search()`
#> elevation (dbl), elevationAccuracy (dbl), stateProvince (chr), year
#> (int), month (int), day (int), eventDate (chr), lastInterpreted
#> (chr), identifiers (chr), facts (chr), relations (chr), geodeticDatum
#> (chr), class (chr), countryCode (chr), country (chr), recordNumber
#> (chr), rights (chr), municipality (chr), rightsHolder (chr),
#> ownerInstitutionCode (chr), type (chr), occurrenceID (chr),
#> collectionCode (chr), identifiedBy (chr), gbifID (chr),
#> occurrenceRemarks (chr), institutionCode (chr), datasetName (chr),
#> catalogNumber (chr), recordedBy (chr), locality (chr), language
#> (chr), identifier (chr), modified (chr), references (chr),
#> verbatimEventDate (chr), verbatimLocality (chr),
#> http...unknown.org.occurrenceDetails (chr), taxonID (chr), eventTime
#> (chr), identificationID (chr), coordinateAccuracy (dbl), depth (dbl),
#> depthAccuracy (dbl), county (chr), informationWithheld (chr),
#> verbatimElevation (chr), georeferenceSources (chr), habitat (chr),
#> fieldNotes (chr)
#> (chr), class (chr), countryCode (chr), country (chr), rightsHolder
#> (chr), identifier (chr), recordNumber (chr), locality (chr),
#> municipality (chr), datasetName (chr), gbifID (chr), collectionCode
#> (chr), language (chr), occurrenceID (chr), type (chr), catalogNumber
#> (chr), recordedBy (chr), institutionCode (chr), rights (chr),
#> ownerInstitutionCode (chr), occurrenceRemarks (chr), identifiedBy
#> (chr), modified (chr), references (chr), verbatimEventDate (chr),
#> verbatimLocality (chr), taxonID (chr),
#> http...unknown.org.occurrenceDetails (chr), eventTime (chr),
#> identificationID (chr), informationWithheld (chr), coordinateAccuracy
#> (dbl), depth (dbl), depthAccuracy (dbl), county (chr), continent
#> (chr), nomenclaturalCode (chr), dataGeneralizations (chr),
#> verbatimCoordinateSystem (chr), datasetID (chr), accessRights (chr),
#> bibliographicCitation (chr)
```

## Examine issues
Expand Down Expand Up @@ -154,24 +155,24 @@ Now that we know a bit about GBIF issues, you can parse your data based on issue
```r
res %>%
occ_issues(gass84)
#> Records found [20650]
#> Records returned [100]
#> Records found [21517]
#> Records returned [97]
#> No. unique hierarchies [1]
#> No. media records [36]
#> No. media records [60]
#> Args [taxonKey=3119195, limit=100, offset=0, fields=all]
#> First 10 rows of data
#>
#> name key decimalLatitude decimalLongitude
#> 1 Helianthus annuus 1095851641 0.00000 0.00000
#> 2 Helianthus annuus 1088900309 33.95239 -117.32011
#> 3 Helianthus annuus 1088933055 25.66564 -100.30348
#> 4 Helianthus annuus 1088909392 24.72449 -99.54020
#> 5 Helianthus annuus 1088937716 25.81691 -100.05940
#> 6 Helianthus annuus 1088944416 26.20518 -98.26725
#> 7 Helianthus annuus 1090389390 59.96150 17.71060
#> 8 Helianthus annuus 1092889365 32.71840 -114.75603
#> 9 Helianthus annuus 1092889645 1.27617 103.79136
#> 10 Helianthus annuus 1098903927 29.17958 -102.99551
#> 4 Helianthus annuus 1135523136 33.96709 -117.99769
#> 5 Helianthus annuus 1088944416 26.20518 -98.26725
#> 6 Helianthus annuus 1092901911 30.22344 -97.95281
#> 7 Helianthus annuus 1098903927 29.17958 -102.99551
#> 8 Helianthus annuus 1135523412 33.96787 -118.00016
#> 9 Helianthus annuus 1092894334 34.16052 -119.03794
#> 10 Helianthus annuus 1092889365 32.71840 -114.75603
#> 11 Helianthus annuus 1090389390 59.96150 17.71060
#> .. ... ... ... ...
#> Variables not shown: issues (chr), datasetKey (chr), publishingOrgKey
#> (chr), publishingCountry (chr), protocol (chr), lastCrawled (chr),
Expand All @@ -184,19 +185,20 @@ res %>%
#> elevation (dbl), elevationAccuracy (dbl), stateProvince (chr), year
#> (int), month (int), day (int), eventDate (chr), lastInterpreted
#> (chr), identifiers (chr), facts (chr), relations (chr), geodeticDatum
#> (chr), class (chr), countryCode (chr), country (chr), recordNumber
#> (chr), rights (chr), municipality (chr), rightsHolder (chr),
#> ownerInstitutionCode (chr), type (chr), occurrenceID (chr),
#> collectionCode (chr), identifiedBy (chr), gbifID (chr),
#> occurrenceRemarks (chr), institutionCode (chr), datasetName (chr),
#> catalogNumber (chr), recordedBy (chr), locality (chr), language
#> (chr), identifier (chr), modified (chr), references (chr),
#> verbatimEventDate (chr), verbatimLocality (chr),
#> http...unknown.org.occurrenceDetails (chr), taxonID (chr), eventTime
#> (chr), identificationID (chr), coordinateAccuracy (dbl), depth (dbl),
#> depthAccuracy (dbl), county (chr), informationWithheld (chr),
#> verbatimElevation (chr), georeferenceSources (chr), habitat (chr),
#> fieldNotes (chr)
#> (chr), class (chr), countryCode (chr), country (chr), rightsHolder
#> (chr), identifier (chr), recordNumber (chr), locality (chr),
#> municipality (chr), datasetName (chr), gbifID (chr), collectionCode
#> (chr), language (chr), occurrenceID (chr), type (chr), catalogNumber
#> (chr), recordedBy (chr), institutionCode (chr), rights (chr),
#> ownerInstitutionCode (chr), occurrenceRemarks (chr), identifiedBy
#> (chr), modified (chr), references (chr), verbatimEventDate (chr),
#> verbatimLocality (chr), taxonID (chr),
#> http...unknown.org.occurrenceDetails (chr), eventTime (chr),
#> identificationID (chr), informationWithheld (chr), coordinateAccuracy
#> (dbl), depth (dbl), depthAccuracy (dbl), county (chr), continent
#> (chr), nomenclaturalCode (chr), dataGeneralizations (chr),
#> verbatimCoordinateSystem (chr), datasetID (chr), accessRights (chr),
#> bibliographicCitation (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.
Expand All @@ -207,24 +209,24 @@ Next, we can remove data with certain issues just as easily by using a `-` sign
```r
res %>%
occ_issues(-depunl, -mdatunl)
#> Records found [20650]
#> Records returned [53]
#> Records found [21517]
#> Records returned [59]
#> No. unique hierarchies [1]
#> No. media records [36]
#> No. media records [60]
#> Args [taxonKey=3119195, limit=100, offset=0, fields=all]
#> First 10 rows of data
#>
#> name key decimalLatitude decimalLongitude
#> 1 Helianthus annuus 1095851641 0.00000 0.00000
#> 2 Helianthus annuus 1088900309 33.95239 -117.32011
#> 3 Helianthus annuus 1088933055 25.66564 -100.30348
#> 4 Helianthus annuus 1088909392 24.72449 -99.54020
#> 5 Helianthus annuus 1088937716 25.81691 -100.05940
#> 6 Helianthus annuus 1088944416 26.20518 -98.26725
#> 8 Helianthus annuus 1092889365 32.71840 -114.75603
#> 9 Helianthus annuus 1092889645 1.27617 103.79136
#> 10 Helianthus annuus 1098903927 29.17958 -102.99551
#> 11 Helianthus annuus 1092901911 30.27181 -97.83409
#> 3 Helianthus annuus 1135826959 NA NA
#> 4 Helianthus annuus 1135523136 33.96709 -117.99769
#> 5 Helianthus annuus 1088944416 26.20518 -98.26725
#> 6 Helianthus annuus 1092901911 30.22344 -97.95281
#> 7 Helianthus annuus 1098903927 29.17958 -102.99551
#> 8 Helianthus annuus 1135523412 33.96787 -118.00016
#> 9 Helianthus annuus 1092894334 34.16052 -119.03794
#> 10 Helianthus annuus 1092889365 32.71840 -114.75603
#> .. ... ... ... ...
#> Variables not shown: issues (chr), datasetKey (chr), publishingOrgKey
#> (chr), publishingCountry (chr), protocol (chr), lastCrawled (chr),
Expand All @@ -237,19 +239,20 @@ res %>%
#> elevation (dbl), elevationAccuracy (dbl), stateProvince (chr), year
#> (int), month (int), day (int), eventDate (chr), lastInterpreted
#> (chr), identifiers (chr), facts (chr), relations (chr), geodeticDatum
#> (chr), class (chr), countryCode (chr), country (chr), recordNumber
#> (chr), rights (chr), municipality (chr), rightsHolder (chr),
#> ownerInstitutionCode (chr), type (chr), occurrenceID (chr),
#> collectionCode (chr), identifiedBy (chr), gbifID (chr),
#> occurrenceRemarks (chr), institutionCode (chr), datasetName (chr),
#> catalogNumber (chr), recordedBy (chr), locality (chr), language
#> (chr), identifier (chr), modified (chr), references (chr),
#> verbatimEventDate (chr), verbatimLocality (chr),
#> http...unknown.org.occurrenceDetails (chr), taxonID (chr), eventTime
#> (chr), identificationID (chr), coordinateAccuracy (dbl), depth (dbl),
#> depthAccuracy (dbl), county (chr), informationWithheld (chr),
#> verbatimElevation (chr), georeferenceSources (chr), habitat (chr),
#> fieldNotes (chr)
#> (chr), class (chr), countryCode (chr), country (chr), rightsHolder
#> (chr), identifier (chr), recordNumber (chr), locality (chr),
#> municipality (chr), datasetName (chr), gbifID (chr), collectionCode
#> (chr), language (chr), occurrenceID (chr), type (chr), catalogNumber
#> (chr), recordedBy (chr), institutionCode (chr), rights (chr),
#> ownerInstitutionCode (chr), occurrenceRemarks (chr), identifiedBy
#> (chr), modified (chr), references (chr), verbatimEventDate (chr),
#> verbatimLocality (chr), taxonID (chr),
#> http...unknown.org.occurrenceDetails (chr), eventTime (chr),
#> identificationID (chr), informationWithheld (chr), coordinateAccuracy
#> (dbl), depth (dbl), depthAccuracy (dbl), county (chr), continent
#> (chr), nomenclaturalCode (chr), dataGeneralizations (chr),
#> verbatimCoordinateSystem (chr), datasetID (chr), accessRights (chr),
#> bibliographicCitation (chr)
```

## Expand issue codes to full names
Expand All @@ -270,7 +273,7 @@ head(out$data[,c(1,5)])
#> issues
#> 1 COUNTRY_COORDINATE_MISMATCH,GEODETIC_DATUM_ASSUMED_WGS84,ZERO_COORDINATE
#> 2 COUNTRY_DERIVED_FROM_COORDINATES,GEODETIC_DATUM_ASSUMED_WGS84
#> 3 COORDINATE_ROUNDED,COUNTRY_DERIVED_FROM_COORDINATES,GEODETIC_DATUM_ASSUMED_WGS84
#> 3
#> 4 COORDINATE_ROUNDED,COUNTRY_DERIVED_FROM_COORDINATES,GEODETIC_DATUM_ASSUMED_WGS84
#> 5 COORDINATE_ROUNDED,COUNTRY_DERIVED_FROM_COORDINATES,GEODETIC_DATUM_ASSUMED_WGS84
#> 6 COORDINATE_ROUNDED,COUNTRY_DERIVED_FROM_COORDINATES,GEODETIC_DATUM_ASSUMED_WGS84
Expand All @@ -290,7 +293,7 @@ head(out$data[,c(1,5:10)])
#> name cucdmis gass84 zerocd cudc cdround depunl
#> 1 Helianthus annuus y y y n n n
#> 2 Helianthus annuus n y n y n n
#> 3 Helianthus annuus n y n y y n
#> 3 Helianthus annuus n n n n n n
#> 4 Helianthus annuus n y n y y n
#> 5 Helianthus annuus n y n y y n
#> 6 Helianthus annuus n y n y y n
Expand All @@ -314,14 +317,14 @@ head(out$data[,c(1,5:10)])
#> GEODETIC_DATUM_ASSUMED_WGS84 ZERO_COORDINATE
#> 1 y y
#> 2 y n
#> 3 y n
#> 3 n n
#> 4 y n
#> 5 y n
#> 6 y n
#> COUNTRY_DERIVED_FROM_COORDINATES COORDINATE_ROUNDED DEPTH_UNLIKELY
#> 1 n n n
#> 2 y n n
#> 3 y y n
#> 3 n n n
#> 4 y y n
#> 5 y y n
#> 6 y y n
Expand Down
2 changes: 1 addition & 1 deletion inst/vign/rgbif_vignette.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,7 @@ head(name_lookup(query='mammalia', return = 'data'))
Look up the species Helianthus annuus

```{r name_lookup3}
head(name_lookup('Helianthus annuus', rank="species", return = 'data'))
head(name_lookup(query = 'Helianthus annuus', rank="species", return = 'data'))
```

The function `name_usage()` works with lots of different name endpoints in GBIF, listed at [http://www.gbif.org/developer/species#nameUsages](http://www.gbif.org/developer/species#nameUsages).
Expand Down
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