Analyzing Gene Tree Quartets under the Multi-Species Coalescent

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Documentation for package ‘MSCquartets’ version 1.1.0

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MSCquartets-package Multispecies Coalescent Model Quartet Package
dataGeneTreeSample Simulated gene tree dataset from species tree
dataHeliconiusMartin Heliconius gene tree dataset
dataYeastRokas Yeast gene tree dataset
estimateEdgeLengths Estimate edge lengths on a species tree from gene tree quartet counts
expectedCFs Produce table of expected quartet concordance factors for a species tree
HolmBonferroni Apply Holm-Bonferroni method to adjust for multiple tests
NANUQ Apply NANUQ network inference algorithm to gene tree data
NANUQdist Compute NANUQ distance and write to file
nexusDist Write a distance table to a file in nexus format
powerDivStat Power divergence statistic of Cressie & Read
pvalHist Plot histogram of log p-values in table
QDC Compute Quartet Distance Consensus tree from gene tree data
QDS Compute Quartet Distance Supertree
quartetDist Compute quartet distance between taxa
quartetNetworkDist Compute network quartet distance between taxa
quartetStarTest Hypothesis test for quartet counts fitting a star tree under the MSC
quartetStarTestInd Multiple independent hypothesis tests for gene quartet counts fitting a species quartet star tree under the MSC
quartetTable Produce table of counts of quartets displayed on trees
quartetTableCollapse Reduce quartet table by combining some taxa
quartetTableDominant Produce table of dominant quartets, with estimates of internal edge lengths
quartetTableParallel Produce table of counts of quartets displayed on trees, in parallel for large data sets
quartetTablePrint Print a quartet table with nice formatting
quartetTableResolved Modify quartet table to show only resolved quartets
quartetTestPlot Produce simplex plot with results of quartet hypothesis tests
quartetTreeErrorProb Bayesian posterior probability of error in 4-taxon unrooted species tree topology estimate
quartetTreeTest Hypothesis test for quartet counts fitting a tree under the MSC
quartetTreeTestInd Multiple independent hypothesis tests for quartet counts fitting a species tree under the MSC
quartetWeightedDist Compute the Weighted Quartet Distance between taxa
simplexCoords Convert 3-d coordinates to 2-d probability simplex coordinates
simplexLabels Label vertices of 2-d probability simplex
simplexPoint Plot point in 2-d probability simplex
simplexPrepare Draw 2-d probability simplex, with model lines for T3 or T1 model
simplexSegment Plot line segment in 2-d probability simplex
simplexText Add text at a point in 2-d probability simplex
T1density Probability density function for Model T1 of Mitchell et al. (2019), Proposition 5.2
T3density Probability density function for Model T3 of Mitchell et al. (2019), Proposition 4.2
taxonNames Get all taxon names from a collection of trees
WQDC Compute Weighted Quartet Distance Consensus tree from gene tree data
WQDCrecursive Compute the Recursive Weighted Quartet Distance Consensus tree from gene tree data
WQDS Compute the Weighted Quartet Distance Supertree
WQDSAdjustLengths Adjust edge lengths on tree built from Weighted Quartet distance to estimate metric tree