Analyzing Gene Tree Quartets under the Multi-Species Coalescent

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Documentation for package ‘MSCquartets’ version 3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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MSCquartets-package	Multispecies Coalescent Model Quartet Package
allPerms	Generate permutations
blobDistance	Compute empirical distance between taxon groups.
BQinference	Main loop of B-quartet inference
circHybOrders	Generate all circular orders with designated hybrid
collapseEdges	Collapse short tree edges
combineCycleResolutions	Combine several cycle resolutions on a tree of blobs to create a network
compatibleSplits	Extract compatible splits
cutDensity	Probability density function for Cut Model
dataGeneTreeSample	Simulated gene tree dataset from species tree
dataPapioniniVanderpool	Papionini 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
expmodNANUQCycleDist	Expected modNANUQ cycle distance
expNANUQCycleDist	Expected NANUQ cycle distance
fitCycleOrders	Compute fit of circular orders to distance with least squares
HolmBonferroni	Apply Holm-Bonferroni method to adjust for multiple tests
initBquartets	Initialize vector of B quartets
labelIntNodes	Label internal nodes on tree
M0	Modified Struve function
MSCquartets	Multispecies Coalescent Model Quartet Package
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
nodeGroups	Groups taxa by deleting a node in a tree
ordersHeuristicmodNANUQ	Choose cycle orders heuristically from empirical modNANUQ distance
powerDivStat	Power divergence statistic of Cressie & Read
pTableYeastRokas	pTable for Yeast dataset
pvalHist	Plot histogram of log p-values in table
QDC	Compute Quartet Distance Consensus tree from gene tree data
QDS	Compute Quartet Distance Supertree
quartetBTinferencePlot	Produce simplex plot with results of B/T-quartet inference
quartetCutMLE	Maximum likelihood estimate of quartet tree of blobs topology and CF under Cut model
quartetCutTest	Hypothesis test for quartet counts fitting a resolved quartet tree of blobs under NMSC
quartetCutTestInd	Multiple independent hypothesis tests for quartet counts fitting the Cut model under the NMSC
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
quartetTallyCpp	Build quartet table from distances
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
resolveCycle	Resolve a node on a tree of blobs as a cycle
resolveLevel1	Resolve Tree of Blobs to Level-1 network
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
sortQuartetTableRows	Sort quartet table rows by lex order
T1density	Probability density function for Model T1
T3density	Probability density function for Model T3
tableHeleconiusMartin	Quartet table for Heliconius gene tree dataset
tableHeliconiusMartin	Quartet table for Heliconius gene tree dataset
tableLeopardusLescroart	Quartet table for Leopardus dataset
taxonNames	Get all taxon names from a collection of trees
TINNIK	TINNIK algorithm to infer species tree of blobs
TINNIKdist	Compute TINNIK distance from quartets and hypothesis test p-values
topDist	Topological distances on a tree
treeFromSplits	Produce tree from compatible splits
treeOfBlobs	Tree of blobs for a network
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