ade4: randtest – R documentation

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randtest

Class of the Permutation Tests (in C).

Description

randtest is a generic function. It proposes methods for the following objects between, discrimin, coinertia ...

Usage

randtest(xtest, ...)
as.randtest(sim, obs, alter = c("greater", "less", "two-sided"), 
  output = c("light", "full"), call = match.call(), subclass = NULL)

## S3 method for class 'randtest'
plot(x, nclass = 10, coeff = 1, ...)
## S3 method for class 'randtest'
print(x, ...)

Arguments

`xtest`	an object used to select a method
`x`	an object of class `randtest`
`...`	further arguments passed to or from other methods; in `plot.randtest` to `hist`
`output`	a character string specifying if all simulations should be stored (`"full"`). This was the default until `ade4` 1.7-5. Now, by default (`"light"`), only the distribution of simulated values is stored in element `plot` as produced by the `hist` function.
`nclass`	a number of intervals for the histogram. Ignored if object output is `"light"`
`coeff`	to fit the magnitude of the graph. Ignored if object output is `"light"`
`sim`	a numeric vector of simulated values
`obs`	a numeric vector of an observed value
`alter`	a character string specifying the alternative hypothesis, must be one of "greater" (default), "less" or "two-sided"
`call`	a call order
`subclass`	a character vector indicating the subclasses associated to the returned object

Details

If the alternative hypothesis is "greater", a p-value is estimated as: (number of random values equal to or greater than the observed one + 1)/(number of permutations + 1). The null hypothesis is rejected if the p-value is less than the significance level. If the alternative hypothesis is "less", a p-value is estimated as: (number of random values equal to or less than the observed one + 1)/(number of permutations + 1). Again, the null hypothesis is rejected if the p-value is less than the significance level. Lastly, if the alternative hypothesis is "two-sided", the estimation of the p-value is equivalent to the one used for "greater" except that random and observed values are firstly centered (using the average of random values) and secondly transformed to their absolute values. Note that this is only suitable for symmetric random distribution.

Value

as.randtest returns a list of class randtest.
plot.randtest draws the simulated values histograms and the position of the observed value.

Examples

par(mfrow = c(2,2))
for (x0 in c(2.4,3.4,5.4,20.4)) {
  l0 <- as.randtest(sim = rnorm(200), obs = x0)
  print(l0)
  plot(l0,main=paste("p.value = ", round(l0$pvalue, dig = 5)))
}
par(mfrow = c(1,1))

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release