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 |
suppressNetBinaryNodes | Suppress Network Binary Nodes |
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 |