penvs_userBgExtent: user provided background extent

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.

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.

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).

Author

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

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

Andrea Paz <paz.andreita@gmail.com>

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

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)
#> Reading layer `Bassaricyon_neblina' from data source 
#>   `/home/runner/work/_temp/Library/wallace/extdata/shp/Bassaricyon_neblina.shp' 
#>   using driver `ESRI Shapefile'
#> Simple feature collection with 1 feature and 1 field
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -79.47486 ymin: -1.15418 xmax: -74.50839 ymax: 6.83333
#> CRS:           NA
#> Study extent user-defined polygon buffered by 0.2 degrees.