Mrpp {asbio}R Documentation

Multi-response permutation procedure. A wrapper for mrpp from vegan.

Description

While mrpp in library vegan directly tests the hypothesis of identical multivariate disributions using a permutation procedure, PC-ORD approximates the distribution of using a Pearson type III distribution which accommodates the fact that the permutation distribution is often significantly skewed (McCune and Grace 2002). The Pearson type III distribution is similar to the binomial distribution when p neq q (Abramowitz and Stegun 1972).

Usage


Mrpp(dat, grouping, permutations = 1000, distance = "euclidean", weight.type = 1, strata)

Arguments

dat data matrix or data frame in which rows are samples and columns are response variable(s), or a dissimilarity object or a symmetric square matrix of dissimilarities.
grouping Factor or numeric index for grouping observations.
permutations Factor or numeric index for grouping observations.
distance Choice of distance metric that measures the dissimilarity between two observations . The function vegdist is used to calculate dissimilarities.
weight.type choice of group weights. See Details below for options.
strata An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata.

Details

Mrpp provides additional output to mrpp including a T statistic and a Pearson's type III p-value. The Pearson Type III distribution has three parameters: a mean, standard deviation , and a shape parameter , based on the skewness of the empirical distribution. These are estimated, and p-values are calculated in the wrapper function Mrpp using functions from the library lmomco (Asquith 2008). See documentation from mrpp for additional information.

Value

The function returns a list of class Mrpp with following items:

call Function call.
delta The overall weighted mean of group mean distances.
E.delta expected delta, under the null hypothesis of no group structure. This is the mean of original dissimilarities.
CS Classification strength (Van Sickle 1997) with weight.type = 3 and NA with other weights.
n Number of observations in each class.
classdelta Mean dissimilarities within classes. The overall delta is the weighted average of these values with given weight.type.
Pvalue Significance of the test.
distance Choice of distance metric used; the "method" entry of the dist object.
weight.type The choice of group weights used.
boot.deltas The vector of "permuted deltas," the deltas calculated from each of the permuted datasets.
permutations The number of permutations used.

Author(s)

M. Herny H. Stevens HStevens@muohio.edu and Jari Oksanen. Wrapper created by Ken Aho

References

McCune, B. and Grace, J. B. (2002) Analysis of Ecological Communities. MjM Software Design, Gleneden Beach, Oregon, USA.

Mielke P. W. and Berry, K. J. (2001) Permutation Methods: A Distance Function Approach. Springer Series in Statistics. Springer.

Van Sickle, J. (1997) Using mean similarity dendrograms to evaluate classifications. Journal of Agricultural, Biological, and Environmental Statistics 2:370-388.

Examples

library(vegan)
data(dune)
data(dune.env)
Mrpp(dune, dune.env$Management)

[Package asbio version 0.1 Index]