PhyloMeasures: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures

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Given a phylogenetic tree T and a sample 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 the implementations of efficient algorithms for several such measures. Most importantly, the package includes algorithms for computing exactly and efficiently the expectation and the variance of these measures, which are essential for null model comparisons. Efficient computation of richness-standardized versions of these metrics, such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures are also available in this package. 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.

Author
Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Date of publication
2015-04-08 00:39:07
Maintainer
Constantinos Tsirogiannis <analekta@gmail.com>
License
GPL-3
Version
1.1

View on CRAN

Man pages

cac.moments
Computes the statistical moments of the Core Ancestor Cost...
cac.query
Computes the (standardised) value of the Core Ancestor Cost...
cbl.moments
Computes the moments of the Common Branch Length measure
cbl.query
Computes the (standardised) value of the Common Branch Length...
cd.moments
Computes the moments of the Community Distance measure
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 (standardised) value of the Community Distance...
mntd.moments
Computes the moments of the Mean Nearest Taxon Distance...
mntd.query
Computes the (standardised) value of the Mean Nearest Taxon...
mpd.moments
Computes the moments of the Mean Pairwise Distance measure
mpd.query
Computes the (standardised) value of the Mean Pairwise...
pd.moments
Computes the moments of the Phylogenetic Diversity measure
pd.query
Computes the (standardised) 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

Files in this package

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/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/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/Unique_fraction.h
PhyloMeasures/src/Measures/Common_branch_length.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/Community_distance.h
PhyloMeasures/src/Measures/Community_distance_impl.h
PhyloMeasures/src/Measures/Mean_nearest_taxon_distance_impl.h
PhyloMeasures/src/Measures/Measure_base.h
PhyloMeasures/src/Measures/Community_distance_nearest_taxon_impl.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/Phylogenetic_measures_kernel.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.query.Rd
PhyloMeasures/man/cd.query.Rd
PhyloMeasures/man/phylosor.query.Rd
PhyloMeasures/man/cac.moments.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