Use in phylogenetic analysis: to identify congruence among distance matrices (D) representing different genes or different types of data. Congruent D matrices correspond to data tables that can be used together in a combined phylogenetic or other type of multivariate analysis.
}
\usage{
-CADM.global(Dmat, nmat, n, nperm=99, make.sym=TRUE, weights=NULL, silent=FALSE)
-CADM.post (Dmat, nmat, n, nperm=99, make.sym=TRUE, weights=NULL, mult="holm", mantel=FALSE, silent=FALSE)
+CADM.global(Dmat, nmat, n, nperm=99, make.sym=TRUE, weights=NULL,
+ silent=FALSE)
+CADM.post (Dmat, nmat, n, nperm=99, make.sym=TRUE, weights=NULL,
+ mult="holm", mantel=FALSE, silent=FALSE)
}
\arguments{
The Holm correction is computed after ordering the P-values in a list with the smallest value to the left. Compute adjusted P-values as:
-\eqn{P_corr = (k-i+1)*P}
+\deqn{P_{corr} = (k-i+1)*P}{P_corr = (k-i+1)*P}
-where i is the position in the ordered list. Final step: from left to right, if an adjusted P_corr in the ordered list is smaller than the one occurring at its left, make the smallest one equal to the largest one.
+where i is the position in the ordered list. Final step: from left to right, if an adjusted \eqn{P_{corr}}{P_corr} in the ordered list is smaller than the one occurring at its left, make the smallest one equal to the largest one.
The Sidak correction is:
-\eqn{P_corr = 1 - (1 - P)^k}
+\deqn{P_{corr} = 1 - (1 - P)^k}{P_corr = 1 - (1 - P)^k}
The Bonferonni correction is:
-\eqn{P_corr = k*P}
+\deqn{P_{corr} = k*P}{P_corr = k*P}
}
\value{
-\code{CADM.global} produces a small table containing the W, Chi2, and Prob.perm statistics described in the following list.
-\code{CADM.post} produces a table stored in element $A_posteriori_tests, containing Mantel.mean, Prob, and Corrected.prob statistics in rows; the columns correspond to the k distance matrices under study, labeled Dmat.1 to Dmat.k.
+\code{CADM.global} produces a small table containing the W, Chi2, and Prob.perm statistics described in the following list.
+\code{CADM.post} produces a table stored in element \code{A_posteriori_tests}, containing Mantel.mean, Prob, and Corrected.prob statistics in rows; the columns correspond to the k distance matrices under study, labeled Dmat.1 to Dmat.k.
If parameter \code{mantel} is TRUE, tables of Mantel statistics and P-values are computed among the matrices.
\item{W }{Kendall's coefficient of concordance, W (Kendall and Babington Smith 1939). }
Siegel, S. and N. J. Castellan, Jr. 1988. Nonparametric statistics for the behavioral sciences. 2nd edition. McGraw-Hill, New York.
}
-\seealso{ \code{\link{kendall.W}}, \code{\link[ape:ape-package]{ape}} }
+
\author{ Pierre Legendre, Universite de Montreal }
\examples{