compseq: Comparison of behavioral (or any) sequences

In sequence: Analysis of Sequences of Events

Description

Compares statistically sequences of states (behavior, texts, molecular data) by likelihood ratio tests on their markovian transition matrices. Performs also a cluster analysis of the sequences and a Principal Coordinates Analysis on the distance matrix between them.

Usage

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

Arguments

ser	list of list: set of sequences
alpha	numeric: global risk threshold for pairwise comparisons.
meth	character:Clustering method. cf hclust.
printdata	Boolean:Print original data.
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: do the cluster analysis.
pca	Boolean: do the 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).
This function does essentially the same work as compmat but with matrices instead of sequences entry.

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

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, flux

Examples

	data(seriseq)
	compseq(seriseq)

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