dens_obj: A wrapper for cRacle::densform where a multi-taxon extraction...

In rsh249/cRacle: Climate Reconstruction Analysis using Coexistence Likelihood Estimation

Description

This function takes extracted climate data (from an object generated by the cRacle::extraction() function) and generates probability density functions for each taxon/variable pair using both a Gaussian (normal) approximation and a Gaussian Kernel Density estimator.

Usage

dens_obj(
  ex,
  clim,
  manip = "condi",
  bw = "nrd0",
  kern = "optcosine",
  clip = 0,
  n = 1024,
  parallel = FALSE,
  nclus = 4,
  bg.n = 200
)

Arguments

ex	An object derived from the extraction() function.
clim	A raster object (see raster::raster() and raster::stack() documentation for reading raster files into R).
manip	Character string of 'reg' for straight likelihood, 'condi' for conditional likelihood statement.
bw	A bandwidth compatible with stats::density(). Options include "nrd", "nrd0", "ucv", "bcv", etc.. Default (and recommended) value is "nrd0".
kern	Type of Kernel to smooth with. Recommend 'gaussian', 'optcosine', or 'epanechnikov'. See: stats::density for options.
clip	A character string of value "range" or "95conf" or "99conf". Should the probability functions be clipped to either the empirical range or the 95 or 99 percent confidence interval?
n	Number of equally spaced points at which the probability density is to be estimated. Defaults to 1024. A lower number increases speed but decreases resolution in the function. A higher number increases resolution at the cost of speed. Recommended values: 512, 1024, 2048, ....
parallel	TRUE or FALSE. Make use of multicore architecture.
nclus	Number of cores to allocate to this function
bg.n	If there is not a background matrix, how many background points PER OCCURRENCE record should be sampled. Default is 1000.

Examples

#distr <- read.table('test_mat.txt', head=T, sep ="\t");
#OR:
data(distr);
data(climondbioclim);
extr.raw = extraction(data=distr, clim= climondbioclim,
 schema='flat', factor = 4, rm.outlier=FALSE);
dens.list.raw <- dens_obj(extr.raw, clim = climondbioclim,
 manip = 'condi', bg.n = 200, bw = 'nrd0', n = 1024);
multiplot(dens.list.raw, names(climondbioclim[[1]]));

rsh249/cRacle documentation built on Feb. 2, 2022, 2:01 p.m.