compmat: Comparison of transition (or succession) matrices

In sequence: Analysis of Sequences of Events

Description

Compares statistically succession matrices by likelihood ratio tests. Performs also a cluster analysis of the sequences and a Pricipal Coordinates Analysis (PCA) on the distance matrix between them.

Usage

compmat(serMat, alpha = 0.05, meth = "ward.D", printdata = FALSE, printdico = FALSE, 
printmat = FALSE, eps = 1e-07, clust = TRUE, pca = TRUE)

Arguments

serMat	List of data.frames. Each of them must contain a matrix of identical dimension, with the same row.names.
alpha	numeric: global risk threshold for pairwise comparisons. Default = 0.05
meth	character: Clustering method. cf hclust.
printdata	Boolean: Print original list of matrices.
printdico	Boolean:Print the dictionnary of states from ser.
printmat	Boolean: print all transition matrices and the consensus matrix.
eps	numeric: precision for the convergence of cmdscale.
clust	Boolean: performs cluster analysis.
pca	Boolean: performs a Principal Coordinates Analysis.

Details

The log likelihood ratio times -2 is used both for tests (Chi-Square approximation followed by Bonferroni post hoc tests) and as a distance to cluster the sequences and to represent them on factorial plans (Principal Coordinates Analysis). Warning: not a metric distance. Susceptible to give incoherent clustering with some methods (meth).

Value

an object of class compseq with attributes

• dico Dictionnary of states

• mdist Matrix of pairwise distances between sequences

• msign Matrix of pairwise significance levels between sequences

• mcom Common or consensus transition matrix

Author(s)

Jean-Sebastien Pierre [e-mail]

References

a Pierre, J. S. and C. Kasper (1990). The Design of Ethological Flow-Charts on Factorial Analysis Representations - an Application to the Study of the Male Mole-Cricket Sexual Courtship. Biology of Behaviour 15(3-4): 125-151.
Van der Heijden, P. G. M. 1986. Transition matrices, model fitting and correspondence analysis. In: Data Analysis and Informatics IV (Ed. by E. Diday), pp. 221-226. Elsevier Science Publishers.

See Also

hclust, cmdscale, ca

Examples

# Compares 10 transition matrices in \code{aphmat} 
data(aphmat)
compmat(aphmat,clust=FALSE,pca=FALSE)

sequence documentation built on March 26, 2020, 7:30 p.m.