makeOccPlot: Make occurrence plot as a PNG file

In peterbat1/RandR.webtool.dataPrep: Tools to prepare data for the R&R Webtool

Make occurrence plot as a PNG file

Description

Produces a PNG image of occurrence records for a selected taxon suitable for use in the R&R webtool

Usage

makeOccPlot(
  taxonNames = NULL,
  extentStr = c("auto", "NSW", "Aust"),
  baseDataPath = NULL,
  useTaxonSubfolders = FALSE,
  outputPath = NULL
)

Arguments

taxonNames	Character array. One or more taxon names to be processed
extentStr	Character. A flag indicating the bounds to which the map will be cropped. Must be one of "auto", "NSW" or "Aust" - see Details for more information
baseDataPath	Character. Path to the folder below which folders for each taxon will be found
useTaxonSubfolders	Logical. Are files in sub-folders using taxonNames entries? Default is FALSE.
outputPath	Character. Path to the folder into which output files will be written using a filename convention described in Details

Details

The function has been designed to work with a fixed structure and filename convention for input data. It is assumed that within the folder defined by the paramater baseDataPath, there is a sub-folder named for each taxon listed in the parameter taxonNames. Then, within each taxon sub-folder there is a file with a name structured as "genus_specificEpithet_herbariumRecords_filtered.csv" which has been produced by the functions fetchALA and filterALA in the package RandR.data.

Output files are placed in the folder defined in paramater outputPath with a name like "genus_specificEpithet_distibution.png". For example, "Neolitsea_dealbata_distribution.png".

The spatial bounds of the output map are set by the parameter extentStr which may have one of three values:

• auto Bounds set to bounding box of the occurrence records with a 0.1 degree buffer

• NSW Bounds set to encompass NSW

• Aust Bounds set to encompass Australia

peterbat1/RandR.webtool.dataPrep documentation built on Jan. 7, 2023, 3:05 p.m.