Description Usage Arguments Examples
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.
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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. |
1 2 3 4 5 6 7 8 9 | #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]]));
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