thin_b: Spatially thin a list of species occurrence data

In HemingNM/ENMwizard: Advanced Techniques for Ecological Niche Modeling Made Easy

Spatially thin a list of species occurrence data

Description

Will use spThin optimisation algorithm to subset the dataset such that all occurrence locations are a minimum distance apart. This process helps reduce the effect of biases in observation records on the predictive performance of ecological niche models.

Usage

thin_b(
  loc.data.lst = list(),
  lat.col = NULL,
  long.col = NULL,
  spec.col = NULL,
  thin.par = 10,
  reps = 10,
  locs.thinned.list.return = TRUE,
  write.files = TRUE,
  max.files = 1,
  write.log.file = TRUE
)

Arguments

loc.data.lst	Named list containing data.frames/SpatialPoints/SpatialPointsDataFrame of species occurence locations. Each data.frame can include several columnns, but must include at minimum a column of latitude and a column of longitude values
lat.col	Name of column of latitude values. Caps sensitive.
long.col	Name of column of longitude values. Caps sensitive.
spec.col	Name of column of species name. Caps sensitive.
thin.par	Thinning parameter - the distance (in kilometers) that you want records to be separated by.
reps	The number of times to repete the thinning process. Given the random process of removing nearest-neighbors there should be 'rep' number of different sets of coordinates.
locs.thinned.list.return	TRUE/FALSE - If true, the 'list' of the data.frame of thinned locs resulting from each replication is returned (see Returns below).
write.files	TRUE/FALSE - If true, new *.csv files will be written with the thinned locs data
max.files	The maximum number of *csv files to be written based on the thinned data
write.log.file	TRUE/FALSE create/append log file of thinning run

Details

Make sure coordinates are in decimal degrees. This function will use great.circle.distance to thin the datasets

Value

Named list containing thinned datasets for each species. See ?thin of spThin package.

See Also

thin, load_thin_occ

Examples

## Not run: 
thinned.dataset.batch <- thin_b(loc.data.lst = spp.occ.list)
plotThin(thinned.dataset.batch[[1]])
length(thinned.dataset.batch[[1]])

## End(Not run)

HemingNM/ENMwizard documentation built on Jan. 4, 2024, 3:24 p.m.