PhyloMeasures: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures

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.

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

View on CRAN

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

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

Files

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

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