thin: Spatially thin species occurence data

In spThin: Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models

Description

thin returns spatially thinned species occurence data sets. A randomizaiton algorithm (thin.algorithm) is used to create data set in which all occurnece locations are at least thin.par distance apart. Spatial thinning helps to reduce the effect of uneven, or biased, species occurence collections on spatial model outcomes.

Usage

thin(
  loc.data,
  lat.col = "LAT",
  long.col = "LONG",
  spec.col = "SPEC",
  thin.par,
  reps,
  locs.thinned.list.return = FALSE,
  write.files = TRUE,
  max.files = 5,
  out.dir,
  out.base = "thinned_data",
  write.log.file = TRUE,
  log.file = "spatial_thin_log.txt",
  verbose = TRUE
)

Arguments

loc.data	A data.frame of occurence locations. It can include several columnns, but must include at minimum a column of latitude values, a column of longitude values, and a column of species names.
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
out.dir	Directory to write new *csv files to
out.base	A file basename to give to the thinned datasets created
write.log.file	TRUE/FALSE create/append log file of thinning run
log.file	Text log file
verbose	TRUE/FALSE - If true, running details of the function are print at the console.

Value

locs.thinned.dfs A list of data.frames, each data.frame the spatially thinned locations of the algorithm for a single replication. This list will have 'reps' elements.

See Also

thin.algorithm

spThin documentation built on Nov. 16, 2019, 1:07 a.m.