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corHMM - Hidden Markov Models of Character Evolution

Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.

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10.18 score 15 stars 2 dependents 564 scripts 2.3k downloads

OUwie - Analysis of Evolutionary Rates in an OU Framework

Estimates rates for continuous character evolution under Brownian motion and Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al. (2012).

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9.47 score 11 stars 210 scripts 969 downloads

hisse - Hidden State Speciation and Extinction

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.

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8.55 score 7 stars 200 scripts 780 downloads

phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

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blastngenbankpeer-reviewedphylogeneticssequence-alignment

6.03 score 25 stars 172 scripts 6 downloads

AnnotationBustR - Extract Subsequences from GenBank Annotations

Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.

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5.39 score 5 stars 11 scripts 1.3k downloads

dietr - Diet Estimated Trophic Levels

Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.

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dietelectivitytrophic

4.48 score 6 stars 375 downloads

MonoPhy - Explore Monophyly of Taxonomic Groups in a Phylogeny

Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) <doi:10.7717/peerj-cs.56>.

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5.08 score 8 stars 30 scripts 395 downloads

TreEvo - Using ABC to Understand Trait Evolution

Various functions for estimating parameters of trait evolution in comparative analyses using Approximate Bayesian Computation.

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4.15 score 1 stars 71 scripts

phrapl - Phylogeography using Approximate Likelihood

This creates and compares models for population structure within a species or between several related species, especially for questions in phylogeography. It can also help delimit populations into species. Models used can range from island models (populations exchanging genes through migration) to phylogeny models (populations splitting with no subsequent gene flow) to anything in between, such as subdivision with some gene flow. Input data are gene tree topologies. Models are fit using approximate likelihood: simulating gene tree evolution many times on the various population trees to estimate the likelihood of seeing the observed gene topologies.

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3.83 score 8 stars 17 scripts

BMhyb - Comparative Methods for Phylogenetic Networks

Analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. This can detect a burst of variation at the formation of a hybrid as well as an increase or decrease in trait value at a hybridization event. Parameters are estimated by maximum likelihood, and model averaging can be done automatically. Users need to enter a comparative data set and a phylogenetic network.

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2.84 score 137 scripts 30 downloads

GDRarity - Implementation of the global model of discretized rarity and its restrictions

GDRarity outlines the global model of discretized rarity and its various restrictions. By integrating geographic, functional trait-based, and phylogenetic dimensions of rarity across regional and local spatial scales, GDRarity characterizes 57 restrictionary frameworks drawn from a global model - some of which include the widely used Rabinowitz rarity, functional rarity, and eco-evolutionary rarity.

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2.70 score 5 scripts

selac - Selection Models for Amino Acid and/or Codon Evolution

Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. Beaulieu et al (2019) <doi:10.1093/molbev/msy222>.

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2.68 score 1 stars 19 scripts 12 downloads

dentist - Dents the Likelihood Surface to Estimate Parameter Uncertainty

This will sample points around a specified distance from the maximum likelihood estimates. This should be a better way to estimate uncertainty than using the Hessian of the likelihood equation. It works by "denting" the likelihood surface to make a ridge at the desired difference in log likelihood and then "walks" around this dented surface, sampling points.

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2.45 score 3 stars 19 scripts

sisters - Runs various sister group comparisons to test hypotheses about diversification

Sister groups are pairs of clades that differ in a key character. If that character leads to higher diversification rate, then clades with that trait should have more species than their sisters. There are several tests to see if this is the case, ranging from a basic sign test to more complex ones (many implemented in the ape package). This package can identify sister groups that differ in a binary trait and perform all the relevant tests. It can also discretize a continuous trait into a binary "high" vs "low" state.

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2.00 score 2 stars 2 scripts

closesamples - Gets feasible taxon samples on a tree

Often you want to pick species at random, but don't have access to all the possible species, and your group might be a nonrandom set. However, you might have a taxonomy, perhaps a bad one, for all the species. This will let you pick species at random on that full taxonomy and then pick a species out of the possible set closest to this. You could still have a biased sample, but way less biased.

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1.70 score

flipped - Applies various odd models for coin flipping

Everyone uses the binomial as the distribution for coin flipping: this assumes for a given coin, the probability of landing heads is constant for all time. It is likely a very sound assumption. However, even for this simple example other models may be possible. This package contains such models.

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1.70 score 5 scripts

popularitree - Subsamples a tree to get popular taxa

Often you want to show a reduced summary tree. Taxa chosen should span all the tree (for example, a tree of mammals should not have just primates) but also be recognizable groups to your audience. This lets you select a final tree size you want, criteria you want to use, and finds the tree that maximizes the criteria.

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1.70 score

RateViz - Visualizations for instantaneous rate matrices

This package uses an instantaneous rate matrix (such as is used for models of DNA evolution, morphological character change over evolutionary history, and other areas) and summarizes it in various ways. These could include bubble plots, a network showing transitions, or calculations to figure out likely paths between two states.

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1.00 score 1 stars 6 scripts