penvs_bgExtent Generate background extent

This function generates a background area according to a user- provided method.

Usage

penvs_bgExtent(occs, bgSel, bgBuf, logger = NULL, spN = NULL)

Arguments

occs: data frame of cleaned or processed occurrences obtained from components occs: Obtain occurrence data or, poccs: Process occurrence data.
bgSel: character. Method of background building. Must be one of three options: 'bounding box' , 'point buffers' or ' minimum convex polygon'.
bgBuf: numeric. Buffer distance in degrees to be used in the building of the background area.
logger: Stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL.
spN: data frame of cleaned occurrences obtained from component occs: Obtain occurrence data. Used to obtain species name for logger messages.

Value

A SpatialPolygons object that contains all occurrences from occs

Details

This function is used in the select study region component. Here, the user can select between three methods ('bounding box', 'point buffers' or ' minimum convex polygon') to determine the background extent based on the observed occurrences. The function returns a SpatialPolygonsDataFrame object of the desired extent.

Author

Jamie Kass <jamie.m.kass@gmail.com>

Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>

Bethany A. Johnson <bjohnso005@citymail.cuny.edu>

Examples

occs <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",
                 package = "wallace"))[, 2:3]
occs$occID <- 1:nrow(occs)
bgExt <- penvs_bgExtent(occs, bgSel = 'bounding box', bgBuf = 0.5)
#> Study extent: bounding box. Buffered by 0.5 degrees.