extractEnvToFile: Extract environmental data

In eliotmiller/ebirdr: Manipulate eBird data

Description

Extract and associate environmental data from GIS layers with eBird records.

Usage

extractEnvToFile(env.wd, ebird.wd, write.wd, keep, longitude, latitude,
  cut.incomplete = TRUE, cores)

Arguments

env.wd	Working directory where the environmental data is currently stored. It would be very easy to make this able to download environmental data, set the resolution you want in the data, and to use other forms of environmental data besides bioclim, but those things are currently hardwired in. It won't be much more work to make this more flexible when we're ready to take that step.
ebird.wd	Working directory where the eBird records are stored.
write.wd	Working directory where the eBird records + environmental data will be saved to.
keep	Character vector of column names in the existing eBird records that you would like to be passed along/kept in the cleaned files. Can be set to 'keep.all' in order to keep all columns.
longitude	The name of the column in the eBird data files where the longitude data is kept.
latitude	The name of the column in the eBird data files where the latitude data is kept.
cut.incomplete	Default is TRUE. If a point is missing environmental data, will remove that point before saving out the file.
cores	The number of cores to use for parallel processing. This package currently requires your computer to be able to handle at, the bare minimum, installation of the various parallel processing packages. A forthcoming feature will allow you to specify 'seq' here, and would mean ebirdr could be run even if you can't install the parallel processing software.

Details

There is a lot of room to make this function more flexible. Currently it assumes you have bioclim data in a folder already on your computer at a resolution of 2.5 minutes. There is no reason the function cannot be generalized to download bioclim data at whatever resolution you prefer, and there is no reason it cannot be generalized to extract data from other GIS layers.

Value

Saves data files with associated environmental data to the write.wd, returns a data frame summarizing sample sizes to the workspace.

eliotmiller/ebirdr documentation built on May 14, 2019, 10:33 a.m.