randtest.enfa: Randomisation Test for the Ecological Niche Factor Analysis

In adehabitat: Analysis of Habitat Selection by Animals

Description

randtest.enfa performs a randomisation test for the Ecological Niche Factor analysis (ENFA).

Usage

## S3 method for class 'enfa'
randtest(xtest, nrepet = 999, ...)

Arguments

xtest	an object of class enfa
nrepet	the number of iterations for the randomisation test
...	further arguments to be passed to the generic function randtest

Details

This test is carried out by simulating a random distribution of the species occurrences in the pixels of a map.

At each step of the randomisation procedure, the test randomly allocates the nk occurrences (where nk is the sum of the occurrence vector pr of the object of class enfa) in the Ik pixels of the focus area (where Ik is the length of this occurrence vector).

At each step of the procedure, the first eigenvalue of the ENFA performed on the randomised data set is recomputed. This value provides a criterion to test the pertinence of the ENFA analysis.

Value

returns a list of class randtest

Author(s)

Clement Calenge [e-mail]

References

Manly, B.F.J. (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology. London: Chapman & Hall.

Hirzel, A.H., Hausser, J., Chessel, D. and Perrin, N. (2002) Ecological-niche factor analysis: How to compute habitat suitability maps without absence data? Ecology, 83, 2027–2036.

See Also

enfa

Examples

## Not run: 
data(chamois)
locs <- chamois$locs
map <- chamois$map
map$Vegetation <- NULL
da <- data2enfa(map, locs)
en <- enfa(dudi.pca(da$tab, scannf=FALSE), da$pr, scannf = FALSE)
(tutu <- randtest(en, nrepet = 100))
plot(tutu)

## End(Not run)

Example output

Loading required package: ade4
Loading required package: tkrplot
Loading required package: tcltk
Loading required package: shapefiles
Loading required package: foreign

Attaching package: 'shapefiles'

The following objects are masked from 'package:foreign':

    read.dbf, write.dbf

Loading required package: sp

************************************************
************************************************
THE PACKAGE adehabitat IS NOW DEPRECATED!!!!!!!
 It is dangerous to use it, as bugs will no longer be corrected.
It is now recommended to use the packages adehabitatMA, adehabitatLT, adehabitatHR, and adehabitatHS.
These 4 packages are the future of adehabitat.
 They have a vignette explaining in detail how they can be used.
They implement more methods than adehabitat
They are based on the more common and more clever spatial classes implemented in sp.
Bugs are corrected frequently.
Really, avoid to use the classical adehabitat, unless you have a very good reason for it.

*****THIS IS THE VERY LAST WARNING*****
 This is the last version of adehabitat submitted to CRAN (at the time of writing: 2015-03-27).
 THE NEXT VERSION OF adehabitat WILL JUST BE A VIRTUAL PACKAGE LOADING ALL THE PACKAGES DESCRIBED ABOVE.

Warning messages:
1: no DISPLAY variable so Tk is not available 
2: loading Rplot failed 
Monte-Carlo test
Call: randtest.enfa(xtest = en, nrepet = 100)

Observation: 0.9054191 

Based on 100 replicates
Simulated p-value: 0.8217822 
Alternative hypothesis: greater 

    Std.Obs Expectation    Variance 
-0.99286304  1.01161577  0.01144046 

adehabitat documentation built on Jan. 28, 2018, 5:02 p.m.