getSpecies2: A wrapper function to download and plot a species...
In peteraharrison/PUCA: Provenancing Using Climate Analogues

Description Usage Arguments Details Value Warning Note Author(s) References See Also Examples

A helper function for speciesInPolygon.

1	getSpecies2(species, client, plot = TRUE, region)

`species`	The scientific or common name of a species.
`client`	The API server which to quiry to download distribution records for the selected species. See Details for available clients.
`plot`	Logic whether to plot the distribution of the selected species
`region`	The geographic region where the species occurs - typically the country, i.e. Australia.

This function relies on the ALA4R and rgbif wrapper functions to quarier the API servers to download the distribution records for a specified species. The function first determines whether the species of interest occurs in Australia or outside of Australia. If the species occurs in Australia, then client = "ALA" and the Atlas of Living Australia (ALA) API server is quiried. If the species occurs outside of Australia, then client = "GBIF" and the Global Biodiversty Inforamtion Facility (GBIF) API server is quired. If plot = T, a new plotting window will open and the distirbution of the specified species will be plotted.

Returns a data.frame containing three columns: species, Latitude, Longitude.

The code calls window() when plot = T. On Windows operating systmes, this option is relatively stable. However, on Mac operating systmes, window() can be quite buggy and can cause R to crash.

The ALA4R and rgbif packages are only available from GitHub and are not yet on CRAN. To download these packages, use Hadley Wickham's devtools package. For example:

devtools::install_github("AtlasOfLivingAustralia/ALA4R") for ALA4R

devtools::install_github("ropensci/rgbif") for rgbif

P. A. Harrison

ALA spatail portal (http://spatial.ala.org.au/#)

ALA4R package (https://github.com/AtlasOfLivingAustralia/ALA4R)

GBIF (http://www.gbif.org/)

rgbif package (https://github.com/ropensci/rgbif)

speciesInPolygon, plotMyRegion

# not run

#' library(ALA4R)
library(rgbif)
library(raster)
library(sp)

# Download and plot the distribution for Eucalyptus ovata
# from the ALA server

#tmp <- PUCA::getSpecies2(species = "Eucalyptus ovata", client = "ALA",
#                         plot = TRUE, region = "Australia")

#head(tmp)
#            species Latitude Longitude
# 1 Eucalyptus ovata    -37.3     148.6
# 2 Eucalyptus ovata    -37.3     148.7
# 3 Eucalyptus ovata    -37.5     149.0
# 4 Eucalyptus ovata    -37.5     149.1
# 5 Eucalyptus ovata    -37.5     149.0
# 6 Eucalyptus ovata    -37.5     149.0