add data

man/configuration_ic.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/shift_configuration.R
+\name{configuration_ic}
+\alias{configuration_ic}
+\title{compute the information criterion score for the given configuration}
+\usage{
+configuration_ic(tr, Y, shift.configuration, criterion = c("pBIC", "pBICess",
+  "mBIC", "BIC", "AIC", "AICc"), root.model = c("OUrandomRoot",
+  "OUfixedRoot"))
+}
+\arguments{
+\item{tr}{an ultrametric phylogenetic tree of type phylo with branch lengths.}
+
+\item{Y}{the trait vector/matrix where it is labeled by the species names appear as row names.}
+
+\item{shift.configuration}{the shift positions, i.e. indicies of edges where the estimated shifts occurs.}
+
+\item{criterion}{the information criterion.}
+
+\item{root.model}{the asncestoral state model.}
+}
+\value{
+the information criterion value of the shift configuration.
+}
+\description{
+compute the information criterion score for the given configuration
+}
+\examples{
+library("l1ou");
+data("lizard.traits", "lizard.tree");
+Y <- lizard.traits[,1];
+eModel <- estimate_shift_configuration(lizard.tree, Y);
+ic.score <- configuration_ic(lizard.tree, eModel$Y, eModel$shift.configuration, criterion="pBIC");
+print(ic.score);
+}
+\seealso{
+\code{\link{estimate_shift_configuration}}
+}
+

man/l1ou_bootstrap_support.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/phylogeny_bootstrap.R
+\name{l1ou_bootstrap_support}
+\alias{l1ou_bootstrap_support}
+\title{computes the bootstrap support for the detected shift configuration}
+\usage{
+l1ou_bootstrap_support(tr, model, nItrs = 100, multicore = FALSE,
+  nCores = 2)
+}
+\arguments{
+\item{tr}{an ultrametric phylogenetic tree of type phylo with branch lengths and tip labels.}
+
+\item{model}{the object generetes by function estimate_shift_configuration.}
+
+\item{nItrs}{number of independent iterations (bootstrap independent replicates).}
+
+\item{multicore}{logical. If TRUE, it runs nCores processes in parallel. See details.}
+
+\item{nCores}{desired number of parallel processes.}
+}
+\value{
+vector of size of the number of edges in the tree. Each entry is the proportion of bootstrap replicates for which a shift is detected on the corresponding edge.
+}
+\description{
+computes the bootstrap support for the detected shift configuration
+}
+\details{
+The results of sequential and parallel runs are not necessarily equal, because different seeds might be used for different bootstrap replicates.
+        To change options, like the information criterion or maximum allowed number of shifts, modify model$opt.
+}
+\examples{
+data(lizard.traits, lizard.tree);
+Y <- lizard.traits[,1];
+eModel <- estimate_shift_configuration(lizard.tree, Y);
+result <- l1ou_bootstrap_support(lizard.tree, eModel, nItrs=2);
+print(result);
+}
+\seealso{
+\code{\link{estimate_shift_configuration}}
+}
+