dfcor {simba}R Documentation

Calculate permuted (Mantel) correlations between one and many variables

Description

The function uses permcor2 to calculate permuted correlation on vectors. One vector is compared to various vectors of the same length. Useful e.g. if one variable has to be tested against various variables.

Usage

dfcor(ox, y, method = "pearson", permutations = 1000, ...)

Arguments

ox Numeric vector. If it is a similarity matrix (i.e. a dist object, extract vector via as.vector(x) beforehand).
y A data.frame containing numeric vectors to correlate x with. Number of rows has to equal the length of x
method Method for correlation. Defaults to "pearson". See cor for other possibilities.
permutations Number of permutations. Defaults to 1000, which gives reasonable results and allows to test against alpha = 0.001.
... Further arguments passed to internal functions (i.e. to cor).

Details

dfcor is a wrapper for permcor2, which is usually called as a part of pcol. Here, the numeric vector in x is compared to each column vector of y.

Value

A list with the following:

call The function call
method P-value obtained by testing the initial correlation against the permuted correlation values.
out A table with statistics. See details below.
gesN The included number of cases.
strata The number of variables against which x was tested.
permutations The number of permutations.
The included printing method gives nice output (where information appears in a slightly different order) ending with the table of out. It is based on a data.frame with nrow = ncol(y) giving the statistics for the correlation between x and each column of y as follows.
corr Correlation value (regarding to method).
sig P-value obtained by testing the initial correlation against the permuted correlation values.
nop Number of included pairs. The function tests for complete cases before calculation starts. Pairs containing NA's are not included.
miss Number of missing pairs.

Note

Maybe pcol will get this functionality in future releases.

Author(s)

Gerald Jurasinski

References

Legendre, P, & Legendre, L. (1998) Numerical Ecology. 2nd English Edition. Elsevier.

See Also

For related functions of simba permcor, permcor2, mancor, pcol. Further see mantel of package vegan for a different implementation of permuted correlation on distance matrices.


[Package simba version 0.2-5 Index]