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rgbif_vignette_oldapi.Rmd
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rgbif_vignette_oldapi.Rmd
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<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->
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](http://www.gbif.org/). 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
```r
install.packages("rgbif")
```
```r
library(rgbif)
```
## Counts taxon concept records matching a range of filters.
```r
occurrencecount(scientificname = "Helianthus annuus", coordinatestatus = TRUE,
year = 2005, maxlatitude = 20)
```
```
[1] 138
```
Count many taxa
```r
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
```r
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
```r
dat <- occurrencelist(scientificname = "Accipiter erythronemius", coordinatestatus = TRUE,
maxresults = 10)
gbifdata(dat)
```
```
taxonName occurrenceID country decimalLatitude
1 Accipiter erythronemius 352220558 Argentina -31.133
2 Accipiter erythronemius 213206174 W. Colombia 3.767
3 Accipiter erythronemius 699199195 Argentina -25.861
4 Accipiter erythronemius 699199198 Argentina -25.911
5 Accipiter erythronemius 621073311 Argentina -27.352
6 Accipiter erythronemius 621073312 Argentina -27.352
7 Accipiter erythronemius 621073310 Argentina -27.352
8 Accipiter erythronemius 699199204 Argentina -25.861
9 Accipiter erythronemius 699417490 Guyana 5.267
10 Accipiter erythronemius 686297260 Guyana 5.267
decimalLongitude catalogNumber earliestDateCollected
1 -59.02 YPM ORN 065671 1961-04-30
2 -76.75 Skin-470489 <NA>
3 -54.52 39196 <NA>
4 -54.36 38199 <NA>
5 -65.60 42228 <NA>
6 -65.60 42227 <NA>
7 -65.60 42229 <NA>
8 -54.52 38015 <NA>
9 -60.73 3998 2001-04-03
10 -60.73 93439 2001-04-03
latestDateCollected
1 1961-04-30
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 2001-04-03
10 2001-04-03
```
Search for many species and make a map
```r
splist <- c("Accipiter erythronemius", "Junco hyemalis", "Aix sponsa")
out <- occurrencelist_many(splist, coordinatestatus = TRUE, maxresults = 20)
gbifmap_list(out)
```
## densitylist provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
A simple example
```r
out <- densitylist(originisocountrycode = "US")
gbifmap_dens(out)
```
## Search by taxon to retrieve number of records in GBIF.
```r
taxoncount("Puma concolor")
```
```
[1] 91
```
```r
taxoncount("Helianthus annuus")
```
```
[1] 142
```