SummarizeBM  R Documentation 
Compiles a summary (appropriate moments, conditional moments, information criteria) of parameters of a Brownian motion model at a given time point. The user is recommended to install suggested package PCMBaseCpp which significantly speeds up the calculations (see Details).
SummarizeBM(phyltree, mData, modelParams, t = c(1), dof = NULL, M.error = NULL, predictors = NULL, min_bl = 0.0003)
phyltree 
The phylogeny in 
mData 
A matrix with the rows corresponding to the tip species while the columns correspond to the traits.
The rows should be named by species 
modelParams 
A list of model parameters, as returned in 
t 
A vector of time points at which the summary is to be calculated. This allows for one to study (and plot) the (conditional) mean and covariance as functions of time. The function additionally returns the parameter summary at the tree's height. 
dof 
Number of unknown parameters in the model, can be extracted from the output of

M.error 
An optional measurement error covariance structure. The measurement errors between species are assumed independent. The program tries to recognize the structure of the passed matrix and accepts the following possibilities :
From version 
predictors 
A vector giving the numbers of the columns from

min_bl 
Value to which PCMBase's 
The likelihood calculations are done by the PCMBase package. However, there is a C++ backend, PCMBaseCpp. If it is not available, then the likelihood is calculated slower using pure R. However, with the calculations in C++ up to a 100fold increase in speed is possible (more realistically 1020 times). The PCMBaseCpp package is available from https://github.com/venelin/PCMBaseCpp.
The phyltree_paths()
function enhances the tree for usage by mvSLOUCH
.
Hence, to save time, it is advisable to first do phyltree<mvSLOUCH::phyltree_paths(phyltree)
and only then use it with BrownianMotionModel()
.
From version 2.0.0
of mvSLOUCH the data has to be passed as a matrix.
To underline this the data parameter's name has been changed to mData
.
From version 2.0.0
of mvSLOUCH the parameter calcCI
has been removed.
The package now offers the possibility of bootstrap confidence intervals, see
function parametric.bootstrap
.
A list for each provided time point. See the help of BrownianMotionModel
for
what the summary at each time point is.
Krzysztof Bartoszek
Bartoszek, K. and Pienaar, J. and Mostad. P. and Andersson, S. and Hansen, T. F. (2012) A phylogenetic comparative method for studying multivariate adaptation. Journal of Theoretical Biology 314:204215.
Butler, M.A. and A.A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683695.
Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist 125:115.
Hansen, T.F. and Bartoszek, K. (2012) Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. Systematic Biology 61(3):413425.
Pienaar et al (in prep) An overview of comparative methods for testing adaptation to external environments.
BrownianMotionModel
, simulBMProcPhylTree
, parametric.bootstrap
RNGversion(min(as.character(getRversion()),"3.6.1")) set.seed(12345, kind = "MersenneTwister", normal.kind = "Inversion") ### We will first simulate a small phylogenetic tree using functions from ape. ### For simulating the tree one could also use alternative functions, e.g. sim.bd.taxa ### from the TreeSim package phyltree<ape::rtree(5) ## The line below is not necessary but advisable for speed phyltree<phyltree_paths(phyltree) ### Define Brownian motion parameters to be able to simulate data ### under the Brownian motion model. BMparameters<list(vX0=matrix(0,nrow=3,ncol=1), Sxx=rbind(c(1,0,0),c(0.2,1,0),c(0.3,0.25,1))) ### Now simulate the data. BMdata<simulBMProcPhylTree(phyltree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx) BMdata<BMdata[phyltree$tip.label,,drop=FALSE] ### Recover the parameters of the Brownian motion. BMestim<BrownianMotionModel(phyltree,BMdata) ### Summarize them. BM.summary<SummarizeBM(phyltree,BMdata,BMestim$ParamsInModel,t=c(1), dof=BMestim$ParamSummary$dof) RNGversion(as.character(getRversion())) #\dontrun { ##It takes too long to run this ### Now obtain bootstrap confidence intervals for some parameters. BMbootstrap<parametric.bootstrap(estimated.model=BMestim,phyltree=phyltree, values.to.bootstrap=c("vX0","StS"),,M.error=NULL,numboot=5) }
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