penvs_bgSample: penvs_bgSample Sample background points

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

penvs_bgSample Sample background points

Description

This function samples background points from an area determined by a rasterBrick or RasterStack of environmental layers previously cropped and masked to user determined extent.

Usage

penvs_bgSample(occs, bgMask, bgPtsNum, 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.
bgMask	a RasterStack or a RasterBrick of environmental layers cropped and masked.
bgPtsNum	numeric. Number of points to be sampled from the area, they will be sampled as long as <= non NA cells in any reference layer.
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.

Details

This function is used in the select study region component. Here, a user provided amount of points is randomly sampled from the RasterBrick or RasterStack of environmental variables cropped and masked to a given background extent. The maximum number of points to be sampled is the number of non NA cells in each layer of the reference RasterBrick or RasterStack If the requested number of points is larger than the number of cells in the reference RasterBrick or RasterStack then only a proportion of the requested will be returned.

Value

a dataframe containing point coordinates (longitude and latitude). All points are within the area provided in the RasterBrick or RasterStack (bgMask). Maximum number of points is equal to non NA cells in each layer of the reference brick or stack.

Author(s)

Jamie Kass <[e-mail]>

Gonzalo E. Pinilla-Buitrago <[e-mail]>

See Also

penvs_bgMask, penvs_bgExtent penvs_userBgExtent, penvs_drawBgExtent, randomPoints

Examples

## Not run: 
occs <-  occs_queryDb(spName = "Panthera onca", occDb = "gbif",
                      occNum = 100)
occs <- as.data.frame(occs[[1]]$cleaned)
envs <- envs_worldclim(bcRes = 10,
                       bcSel = c("bio03", "bio04", "bio13", "bio14"),
                       doBrick = TRUE)
bgExt <- penvs_bgExtent(occs, bgSel = 'bounding box', bgBuf = 0.5)
bgMask <- penvs_bgMask(occs, envs, bgExt)
bgsample <- penvs_bgSample(occs, bgMask, bgPtsNum = 1000)

## End(Not run)

wallace documentation built on Sept. 26, 2023, 1:06 a.m.