Man pages for MSCquartets
Analyzing Gene Tree Quartets under the Multi-Species Coalescent
| 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... |
| 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... |
| expectedCFs | Produce table of expected quartet concordance factors for a... |
| 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-package | 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... |
| 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... |
| quartetCutTest | Hypothesis test for quartet counts fitting a resolved quartet... |
| quartetCutTestInd | Multiple independent hypothesis tests for quartet counts... |
| quartetDist | Compute quartet distance between taxa |
| quartetNetworkDist | Compute network quartet distance between taxa |
| quartetStarTest | Hypothesis test for quartet counts fitting a star tree under... |
| quartetStarTestInd | Multiple independent hypothesis tests for gene quartet counts... |
| 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... |
| quartetTableParallel | Produce table of counts of quartets displayed on trees, in... |
| 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... |
| quartetTreeTest | Hypothesis test for quartet counts fitting a tree under the... |
| quartetTreeTestInd | Multiple independent hypothesis tests for quartet counts... |
| 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... |
| 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... |
| 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 |
| 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... |
| 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... |
| WQDCrecursive | Compute the Recursive Weighted Quartet Distance Consensus... |
| WQDS | Compute the Weighted Quartet Distance Supertree |
| WQDSAdjustLengths | Adjust edge lengths on tree built from Weighted Quartet... |
