PhyloMeasures: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures
Version 2.1

Given a phylogenetic tree T and an assemblage S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers efficient algorithms that can process large phylogenetic data for several such measures. Most importantly, the package includes algorithms for computing efficiently the standardized versions of phylogenetic measures and their p-values, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richness-standardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundance-weighted models.

Browse man pages Browse package API and functions Browse package files

AuthorConstantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Date of publication2017-01-14 01:13:19
MaintainerConstantinos Tsirogiannis <tsirogiannis.c@gmail.com>
LicenseGPL-3
Version2.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PhyloMeasures")

Man pages

cac.moments: Computes the statistical moments of the Core Ancestor Cost...
cac.pvalues: Computes the p-values of the Core Ancestor Cost measure
cac.query: Computes the (standardized) value of the Core Ancestor Cost...
cbl.moments: Computes the moments of the Common Branch Length measure...
cbl.query: Computes the (standardized) value of the Common Branch Length...
cd.moments: Computes the moments of the Community Distance measure under...
cdnt.averaged.query: Computes the value of the averaged Community Distance Nearest...
cdnt.directed.query: Computes the value of the directed Community Distance Nearest...
cdnt.query: Computes the value of the maximised Community Distance...
cd.query: Computes the (standardized) value of the Community Distance...
mntd.moments: Computes the moments of the Mean Nearest Taxon Distance...
mntd.pvalues: Computes the p-values of the Mean Nearest Taxon Distance...
mntd.query: Computes the (standardized) value of the Mean Nearest Taxon...
mpd.moments: Computes the moments of the Mean Pairwise Distance measure
mpd.pvalues: Computes the p-values of the Mean Pairwise Distance measure
mpd.query: Computes the (standardized) value of the Mean Pairwise...
pd.moments: Computes the moments of the Phylogenetic Diversity measure
pd.pvalues: Computes the p-values of the unrooted Phylogenetic Diversity...
pd.query: Computes the (standardized) value of the unrooted...
PhyloMeasures-package: PhyloMeasures: Fast Computations of Phylogenetic Biodiversity...
phylosor.query: Computes the value of the Phylogenetic Sorensen's Similarity...
unifrac.query: Computes the value of the Unique Fraction measure

Functions

PhyloMeasures Man page
PhyloMeasures-package Man page
cac.moments Man page Source code
cac.moments.uniform Source code
cac.moments.weighted Source code
cac.pvalues Man page Source code
cac.query Man page Source code
cac.query.uniform Source code
cac.query.weighted Source code
cbl.moments Man page Source code
cbl.query Man page Source code
cd.moments Man page Source code
cd.query Man page Source code
cdnt.averaged.query Man page Source code
cdnt.directed.query Man page Source code
cdnt.query Man page Source code
mntd.moments Man page Source code
mntd.moments.uniform Source code
mntd.moments.weighted Source code
mntd.pvalues Man page Source code
mntd.query Man page Source code
mntd.query.uniform Source code
mntd.query.weighted Source code
mpd.moments Man page Source code
mpd.moments.uniform Source code
mpd.moments.weighted Source code
mpd.pvalues Man page Source code
mpd.query Man page Source code
mpd.query.uniform Source code
mpd.query.weighted Source code
pd.moments Man page Source code
pd.moments.uniform Source code
pd.moments.weighted Source code
pd.pvalues Man page Source code
pd.query Man page Source code
pd.query.uniform Source code
pd.query.weighted Source code
phylosor.query Man page Source code
unifrac.query Man page Source code

Files

tests
tests/test.tre
tests/tests.R
src
src/Phylogenetic_measures.h
src/Numeric_traits_double.h
src/Exception_related_types.h
src/PhyloMeasures.cpp
src/Measures
src/Measures/Poisson_binomial_moments_Phylogenetic_diversity.h
src/Measures/Mean_nearest_taxon_distance.h
src/Measures/Phylogenetic_Sorensens_similarity.h
src/Measures/Phylogenetic_diversity.h
src/Measures/Phylogenetic_diversity_impl.h
src/Measures/Community_distance_nearest_taxon.h
src/Measures/Phylogenetic_Sorensens_similarity_impl.h
src/Measures/Polynomial_related_types.h
src/Measures/Measure_base
src/Measures/Measure_base/Measure_base_unimodal_impl.h
src/Measures/Measure_base/Measure_base_bimodal_impl.h
src/Measures/Measure_base/Mean_pairwise_distance_base_impl.h
src/Measures/Measure_base/Mean_pairwise_distance_base.h
src/Measures/Measure_base/Measure_base_unimodal.h
src/Measures/Measure_base/Measure_base_bimodal.h
src/Measures/Unique_fraction_impl.h
src/Measures/Mean_pairwise_distance_impl.h
src/Measures/Mean_pairwise_distance.h
src/Measures/Polynomial_related_types
src/Measures/Polynomial_related_types/Polynomial_rep.h
src/Measures/Unique_fraction.h
src/Measures/Common_branch_length.h
src/Measures/Poisson_binomial_moments_Mean_nearest_taxon_distance.h
src/Measures/Core_ancestor_cost_impl.h
src/Measures/Core_ancestor_cost.h
src/Measures/Common_branch_length_impl.h
src/Measures/Poisson_binomial_moments_Mean_pairwise_distance.h
src/Measures/Community_distance.h
src/Measures/Community_distance_impl.h
src/Measures/Mean_nearest_taxon_distance_impl.h
src/Measures/Poisson_binomial_types.h
src/Measures/Measure_base.h
src/Measures/Community_distance_nearest_taxon_impl.h
src/Incremental_Monte_Carlo_types
src/Incremental_Monte_Carlo_types/Incremental_Monte_Carlo_handler_impl.h
src/Incremental_Monte_Carlo_types/Incremental_Monte_Carlo_handler.h
src/Tree_node_types
src/Tree_node_types/Community_distance_nearest_taxon_node_type.h
src/Tree_node_types/Tree_node_bimodal.h
src/Tree_node_types/Tree_node_unimodal.h
src/Tree_node_types/Mean_nearest_taxon_distance_node_type.h
src/Tree_node.h
src/Random_samplers.h
src/Numeric_traits_types
src/Numeric_traits_types/Protected_number_type.h
src/Phylogenetic_measures_kernel.h
src/Random_samplers
src/Random_samplers/Uniform_sampler.h
src/Random_samplers/R_style_sampler.h
src/Random_samplers/Sequential_sampler.h
src/Exception_related_types
src/Exception_related_types/Exception_functor.h
src/Exception_related_types/Exception_type.h
src/Phylogenetic_tree_bimodal.h
src/Phylogenetic_tree_base.h
src/Phylogenetic_tree_bimodal_impl.h
src/Phylogenetic_tree_base_impl.h
NAMESPACE
R
R/PhyloMeasures.R
MD5
DESCRIPTION
man
man/pd.query.Rd
man/mpd.query.Rd
man/PhyloMeasures-package.Rd
man/cdnt.query.Rd
man/cdnt.directed.query.Rd
man/cbl.query.Rd
man/cbl.moments.Rd
man/mntd.moments.Rd
man/mntd.query.Rd
man/cac.pvalues.Rd
man/cac.query.Rd
man/cd.query.Rd
man/phylosor.query.Rd
man/cac.moments.Rd
man/pd.pvalues.Rd
man/mntd.pvalues.Rd
man/mpd.moments.Rd
man/cd.moments.Rd
man/unifrac.query.Rd
man/pd.moments.Rd
man/cdnt.averaged.query.Rd
man/mpd.pvalues.Rd
PhyloMeasures documentation built on May 19, 2017, 6:09 p.m.