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DESCRIPTION
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DESCRIPTION
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Package: PMMUsingSPLITT
Type: Package
Title: Calculating the Likelihood of Phylogenetic Mixed Models using the 'SPLITT' Library
Version: 1.0.2
Date: 2019-07-21
Authors@R: person("Venelin", "Mitov", email = "vmitov@gmail.com",
role = c("aut", "cre", "cph"))
Maintainer: Venelin Mitov <vmitov@gmail.com>
Description: Implementation of the log-likelihood calculation of the univariate
phylogenetic mixed model (PMM) using parallel tree traversal. The PMM is
used for comparative analysis of biological data originating from a set of
living and/or extinct species to estimate the rate of phenotypic evolution
resulting from genetic drift. The calculation of the log-likelihood of the
model parameters, given a phylogenetic tree and trait data at the tips, is
done using a quadratic polynomial representation of the log-likelihood
function described in the article "Parallel Likelihood Calculation for
Phylogenetic Comparative Models: the 'SPLITT' C++ Library". A preprint of
the article is available from
<https://www.biorxiv.org/content/early/2018/10/29/235739>.
The package provides an implementation in R (function 'PMMLogLik') as well
as a parallel implementation in C++ (function 'PMMLogLikCpp') based
on the 'SPLITT' library for serial and parallel lineage traversal of trees
(<https://venelin.github.io/SPLITT/index.html>). The function 'MiniBenchmark'
allows to compare the calculation times for different tree sizes.
License: GPL (>= 3.0)
LazyData: true
Encoding: UTF-8
Depends:
R (>= 3.1.0),
Rcpp,
methods
LinkingTo: Rcpp
Imports:
ape
Suggests:
testthat
RoxygenNote: 6.1.1
ByteCompile: yes
NeedsCompilation: yes
URL: https://github.com/venelin/PMMUsingSPLITT, https://venelin.github.io/SPLITT/index.html
BugReports: https://github.com/venelin/PMMUsingSPLITT/issues