geo_findlocal: Search for likely simulated localities with geographic...

Description Usage Arguments Examples

View source: R/search_fun.R

Description

This wraps the search() function within a set of commands that randomly splits the distribution in to 4 quadrants 'n' number of times. For widespread, genetically diverse species this has the effect of applying more locally relevant probability functions to the data.

Usage

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geo_findlocal(ext_ob, clim, type, maxiter = 10, searchrep = 1,
  manip = "condi", alpha = 0, divisions = 10, factor = 4,
  parallel = FALSE, nclus = 2, w = FALSE)

Arguments

ext_ob

A data.frame of climate values (i.e., extracted from the climate raster object). Will be passed to multiv_likelihood().

clim

A raster object of climate data (matching x)

type

Designate either ".gauss" or ".kde".

maxiter

Maximum number of search iterations.

searchrep

How many times to search for simulated localities (per parent occurrence) per iteration. Recommend 1, but feel free to tune this parameter.

manip

Specify either 'reg', 'condi', or 'bayes. Default is 'condi'. See documentation for densform() for descriptions of these.

alpha

The value of alpha to be used to calculate the initial confidence interval for removing climatic outliers in the sample(s).

divisions

How many times should the data be split into quadrants? Default is 5 resulting in 20 (5x4quads) geographically oriented samples to be selected.

factor

To be passed to the extraction() function for post search thinning of data to limit overfitting. Set to 1 to ignore.

parallel

True or False to use parallel computing. This implements each division as embarassingly parallel processes. However, note that this option changes the meaning of the divisions object to the maximum number of division iterations. Fewer iterations may be returned if too few occurrences are selected.

nclus

If parallel is TRUE then set the maximum number of cores to use in the compute cluster. Default is 2.

w

To weight log-likelihoods by the coefficient of variation or not.

Examples

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## Not run: 
data(abies);
head(abies)
ext.abies = extraction(abies, climondbioclim, 
 schema='flat', factor =4,  
 rm.outlier=FALSE);
sea <- geo_findlocal(ext.abies, climondbioclim, 
 type = '.kde', maxiter = 5, 
 searchrep = 1, manip = 'condi', 
 divisions = 8, parallel =TRUE, nclus = 4)
 plot_clim(sea, climondbioclim[[5]])
 
## End(Not run)

rsh249/vegdistmod documentation built on May 28, 2019, 3:31 a.m.