penvs_userBgExtent: penvs_userBgExtent: user provided background extent

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

penvs_userBgExtent: user provided background extent

Description

This function generates a background area according to a user provided polygon and buffer.

Usage

penvs_userBgExtent(
  bgShp_path,
  bgShp_name,
  userBgBuf,
  occs,
  logger = NULL,
  spN = NULL
)

Arguments

bgShp_path	path to the user provided shapefile or csv with vertex coordinates.
bgShp_name	name of the user provided shapefile or csv with vertex coordinates.
userBgBuf	buffer to be used in creating the background extent must be >= 0.
occs	data frame of cleaned or processed occurrences obtained from components occs: Obtain occurrence data or, poccs: Process occurrence data.
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	Species name.

Details

This function is used in the select study region component. Here, the user provides either a shapefile or a csv with vertex coordinates with the desired shape for the background extent, the user may include a buffer to the given polygon. The buffered polygon must include all occurrences (occs) or function will return an error. The function returns a SpatialPolygons object of the desired extent (+ buffer).

Value

This function returns a SpatialPolygons object with the user provided shape (+ a buffer if userBgBuf >0). The polygon will be at least large enough to contain all occurrences.

Author(s)

Jamie Kass <[e-mail]>

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

Andrea Paz <[e-mail]>

See Also

penvs_drawBgExtent, penvs_bgExtent, penvs_bgMask , penvs_bgSample

Examples

occs <- read.csv(system.file("extdata/Bassaricyon_neblina.csv",
                 package = "wallace"))[, 2:3]
occs$occID <- 1:nrow(occs)
pathShp <- list.files(system.file("extdata/shp", package = "wallace"),
                      full.names = TRUE)
nameShp <- list.files(system.file("extdata/shp", package = "wallace"),
                      full.names = FALSE)
userBgbf <- penvs_userBgExtent(bgShp_path = pathShp, bgShp_name = nameShp,
                               userBgBuf = 0.2, occs = occs)

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