densform: Generate standard probability density functions for each...
In rsh249/vegdistmod: Vegetation distribution modeling and spatial informatics

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

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densform(ex, clim, name = "", bw = "nrd0", kern = "gaussian",
  manip = "condi", n = 1024, from = 0, to = 0, clip = 0, bg.n = 10,
  bg = NULL)

`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).
`name`	A character string describing (preferably) the group for which PDFs are being constructed (i.e., a species binomial). If none is supplied, a value of column "tax" is selected as a default.
`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.
`manip`	Character string of 'reg' for intersectional likelihood, 'condi' for conditional likelihood statement.
`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, ....
`from`	vector of starting points by variable. Default is the variable layer minimum.
`to`	vector of ending points by variable. Default is the variable layer maximum.
`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?
`bg.n`	If manip = 'condi'. How many background points PER OCCURRENCE record should be sampled. Default is 1000.
`bg`	Optionally send a matrix of an extraction object to use as the background sample.

## Not run: 
#distr <- read.table('test_mat.txt', head=T, sep ="\t");
data(distr);
data(climondbioclim);
extr.raw = extraction(data=distr, clim= climondbioclim, schema='raw');
extr.sub = subset(extr.raw, extr.raw$tax == extr.raw[5,'tax']);
dens.sub = densform(extr.sub, clim = climondbioclim, bw = 'nrd0', n = 128, bg.n=25);
densplot(dens.sub, names(climondbioclim[[1]]));

## End(Not run)