rgbif tutorial

Note: this vignette works with the current version on CRAN that works with the old GBIF API.

The rgbif package interacts with the API services of the Global Biodiversity Information Facility GBIF. GBIF currently holds 377,177,914 indexed records, ~10K datasets, and 419 publishers (i.e., dataset submitters).

This tutorial will go through three use cases to demonstrate the kinds of things possible in rgbif.

• Counts taxon concept records matching a range of filters.
• Returns summary counts of occurrence records by one-degree cell.
• occurrencelist searches for taxon concept records matching a range of filters.
• densitylist gets density of occurrence records by one-degree cell.
• Search by taxon to retrieve number of records in GBIF.

Install and load package from GitHub

install.packages("rgbif")

library(rgbif)

Counts taxon concept records matching a range of filters.

occurrencecount(scientificname = "Helianthus annuus", coordinatestatus = TRUE, 
    year = 2005, maxlatitude = 20)

[1] 138

Count many taxa

lapply(c("Helianthus debilis", "Abies procera", "Astragalus"), function(x) occurrencecount(scientificname = x, 
    coordinatestatus = TRUE))

[[1]]
[1] 26

[[2]]
[1] 573

[[3]]
[1] 945

Return summary counts of occurrence records by one-degree cell for a single taxon, country, dataset, data publisher or data network

out <- densitylist(originisocountrycode = "CA")
head(gbifdata(out))

  cellid minLatitude maxLatitude minLongitude maxLongitude count
1  46913          40          41          -67          -66    44
2  46914          40          41          -66          -65   519
3  46915          40          41          -65          -64   475
4  46916          40          41          -64          -63   432
5  46917          40          41          -63          -62    55
6  46918          40          41          -62          -61   143

Occurrencelist searches for taxon concept records matching a range of filters.

A simple example

dat <- occurrencelist(scientificname = "Accipiter erythronemius", coordinatestatus = TRUE, 
    maxresults = 10)
gbifdata(dat)

                 taxonName occurrenceID     country decimalLatitude
1  Accipiter erythronemius    699199198   Argentina         -25.911
2  Accipiter erythronemius    621073310   Argentina         -27.352
3  Accipiter erythronemius    621073311   Argentina         -27.352
4  Accipiter erythronemius    699199204   Argentina         -25.861
5  Accipiter erythronemius    621073312   Argentina         -27.352
6  Accipiter erythronemius    699199195   Argentina         -25.861
7  Accipiter erythronemius    213206174 W. Colombia           3.767
8  Accipiter erythronemius    352220558   Argentina         -31.133
9  Accipiter erythronemius    699417490      Guyana           5.267
10 Accipiter erythronemius    686297260      Guyana           5.267
   decimalLongitude  catalogNumber earliestDateCollected
1            -54.36          38199                  <NA>
2            -65.60          42229                  <NA>
3            -65.60          42228                  <NA>
4            -54.52          38015                  <NA>
5            -65.60          42227                  <NA>
6            -54.52          39196                  <NA>
7            -76.75    Skin-470489                  <NA>
8            -59.02 YPM ORN 065671            1961-04-30
9            -60.73           3998            2001-04-03
10           -60.73          93439            2001-04-03
   latestDateCollected
1                 <NA>
2                 <NA>
3                 <NA>
4                 <NA>
5                 <NA>
6                 <NA>
7                 <NA>
8           1961-04-30
9           2001-04-03
10          2001-04-03

Search for many species and make a map

splist <- c("Accipiter erythronemius", "Junco hyemalis", "Aix sponsa")
out <- occurrencelist_many(splist, coordinatestatus = TRUE, maxresults = 20)
gbifmap_list(out)

plot of chunk occurrencelist_many

densitylist provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.

A simple example

out <- densitylist(originisocountrycode = "US")
gbifmap_dens(out)

plot of chunk densitylist2

Search by taxon to retrieve number of records in GBIF.

taxoncount("Puma concolor")

[1] 91

taxoncount("Helianthus annuus")

[1] 142