logLik_CsurosMiklos: Log-likelihood of count data on a phylogenetic tree
In cecileane/WGDgc: Whole genome duplication detection using gene counts

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/logLik_CsurosMiklos.r

Calculates the probability of gene count data on a phylogenetic tree under a birth-and-death process and whole genome duplication (or triplication) events, conditional on n surviving gene lineages at the root. Also computes the probability of a family going extinct.

1 2	logLik_CsurosMiklos(logLamlogMu, nLeaf, nFamily, phyloMat, geneCountData, mMax, wgdTab, edgeOrder)

`logLamlogMu`	vector of size 1 or 2, for the log of the duplication and loss rates. When a single rate is provided, the duplication and loss rates are assumed to be equal.
`nLeaf`	number of present-day species.
`nFamily`	number of gene families.
`phyloMat`	a phylogenetic matrix with 4 columns: parent (ancestor node), child (descendant node), time (branch length), and species names. The number of rows is the number of nodes in the tree.
`geneCountData`	data frame with one column for each species and one row for each family, containing the number of gene copies in each species for each gene family. The column names must match the species names in the tree.
`mMax`	maximum number of surviving lineages at the root, at which the likelihood will be computed.
`wgdTab`	data frame with 5 columns: node before event, event type (WGD or WGT) and retention rates of 1, 2 and 3 gene copies. The number of rows is the number of WGD events.
`edgeOrder`	a data frame listing the tree edges in post-order traversal with information on which are birth-death and WGD/T edges.

`loglikRoot`	matrix of size `nMax+1` by `nFamily` giving the log likelihood of each gene family given that there are n surviving gene lineages at the root in row n+1. Column k corresponds to family k.
`doomedRoot`	probability that a single gene lineage present at the root goes extinct.
`doomedRootLeft`	probability that a single gene lineage at the root goes extinct in the clade on the left side of the root.
`doomedRootRight`	probability that a single gene lineage at the root goes extinct in the clade on the right side of the root.

Cécile Ané

Csuros M and Miklos I (2009). Streamlining and large ancestral genomes in archaea inferred with a phylogenetic birth-and-death model. Molecular Biology and Evolution. 26:2087-2095.

Charles-Elie Rabier, Tram Ta and Cécile Ané (2013). Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Molecular Biology and Evolution. 31(3):750-762.

processInput, getEdgeOrder.

tre.string = "(D:{0,18.03},(C:{0,12.06},(B:{0,7.06},
              A:{0,7.06}):{0,2.49:wgd,0:0,2.50}):{0, 5.97});"
tre.phylo4d = read.simmap(text=tre.string)
dat = data.frame(A=c(2,2,3,1), B=c(3,0,2,1), C=c(1,0,2,2), D=c(2,1,1,1));
a = processInput(tre.phylo4d, startingQ=0.9)
logLik_CsurosMiklos(log(c(.01,.02)), nLeaf=4, nFamily=4,
                    a$phyloMat,dat,mMax=8,a$wgdTab, a$edgeOrder)