The method, which is described in detail in Legendre et al. (2002), requires some estimates of the phylogenetic trees or phylogenetic distances, and also a description of the host-parasite associations (H-P links) observed in nature.
}
\usage{
-parafit(host.D, para.D ,HP ,nperm=999, test.links=FALSE, seed=NULL,
+parafit(host.D, para.D ,HP ,nperm=999, test.links=FALSE, seed=NULL,
correction="none", silent=FALSE)
}
\arguments{
- \item{host.D }{ A matrix of phylogenetic or patristic distances among the hosts. A matrix of patristic distances exactly represents the information in a phylogenetic tree. }
- \item{para.D }{ A matrix of phylogenetic or patristic distances among the parasites. A matrix of patristic distances exactly represents the information in a phylogenetic tree. }
+ \item{host.D }{ A matrix of phylogenetic or patristic distances among the hosts (object class: \code{matrix}, \code{data.frame} or \code{dist}). A matrix of patristic distances exactly represents the information in a phylogenetic tree. }
+ \item{para.D }{ A matrix of phylogenetic or patristic distances among the parasites (object class: \code{matrix}, \code{data.frame} or \code{dist}). A matrix of patristic distances exactly represents the information in a phylogenetic tree. }
\item{HP }{ A rectangular matrix with hosts as rows and parasites as columns. The matrix contains 1's when a host-parasite link has been observed in nature between the host in the row and the parasite in the column, and 0's otherwise. }
\item{nperm}{ Number of permutations for the tests. If \code{nperm =
- 0}, permutation tests will not be computed. The default value is \code{nperm = 999}. For large data files, the permutation test is rather slow since the permutation procedure is not compiled. }
+ 0}, permutation tests will not be computed. The default value is \code{nperm = 999}. For large data files, the permutation test is rather slow since the permutation procedure is not compiled. }
\item{test.links }{ \code{test.links = TRUE} will test the significance of individual host-parasite links. Default: \code{test.links = FALSE}. }
\item{seed }{ \code{seed = NULL} (default): a seed is chosen at random by the function. That seed is used as the starting point for all tests of significance, i.e. the global H-P test and the tests of individual H-P links if they are requested. Users can select a seed of their choice by giving any integer value to \code{seed}, for example \code{seed = -123456}. Running the function again with the same seed value will produce the exact same test results. }
\item{correction}{ Correction methods for negative eigenvalues (details below): \code{correction="lingoes"} and \code{correction="cailliez"}. Default value: \code{"none"}. }
\details{
Two types of test are produced by the program: a global test of coevolution and, optionally, a test on the individual host-parasite (H-P) link.
-The function computes principal coordinates for the host and the parasite distance matrices. The principal coordinates (all of them) act as a complete representation of either the phylogenetic distance matrix or the phylogenetic tree.
+The function computes principal coordinates for the host and the parasite distance matrices. The principal coordinates (all of them) act as a complete representation of either the phylogenetic distance matrix or the phylogenetic tree.
Phylogenetic distance matrices are normally Euclidean. Patristic distance matrices are additive, thus they are metric and Euclidean. Euclidean matrices are fully represented by real-valued principal coordinate axes. For non-Euclidean matrices, negative eigenvalues are produced; complex principal coordinate axes are associated with the negative eigenvalues. So, the program rejects matrices that are not Euclidean and stops.
The \code{print.parafit} function prints out the results of the global test and, optionally, the results of the tests of the individual host-parasite links.
}
-\value{
+\value{
\item{ParaFitGlobal }{The statistic of the global H-P test. }
- \item{p.global }{The permutational p-value associated with the ParaFitGlobal statistic. }
- \item{link.table }{The results of the tests of individual H-P links, including the ParaFitLink1 and ParaFitLink2 statistics and the p-values obtained from their respective permutational tests. }
+ \item{p.global }{The permutational p-value associated with the ParaFitGlobal statistic. }
+ \item{link.table }{The results of the tests of individual H-P links, including the ParaFitLink1 and ParaFitLink2 statistics and the p-values obtained from their respective permutational tests. }
\item{para.per.host }{Number of parasites per host. }
\item{host.per.para }{Number of hosts per parasite. }
\item{nperm }{Number of permutations for the tests. }
\references{
Hafner, M. S, P. D. Sudman, F. X. Villablanca, T. A. Spradling, J. W. Demastes and S. A. Nadler. 1994. Disparate rates of molecular evolution in cospeciating hosts and parasites. \emph{Science}, \bold{265}, 1087--1090.
-Legendre, P., Y. Desdevises and E. Bazin. 2002. A statistical test for host-parasite coevolution. \emph{Systematic Biology}, \bold{51}, 217--234.
+Legendre, P., Y. Desdevises and E. Bazin. 2002. A statistical test for host-parasite coevolution. \emph{Systematic Biology}, \bold{51(2)}, 217--234.
}
\seealso{\code{\link{pcoa}} }
projects / ape.git / blobdiff