getLikGeneCount: Negative log-likelihood of gene count data
In cecileane/WGDgc: Whole genome duplication detection using gene counts

Description Usage Arguments Details Value References See Also Examples

Calculates the overall negative log-likelihood of gene count data on a phylogenetic tree under a birth-and-death process and whole genome duplication events.

getLikGeneCount(para, input, geneCountData, mMax=NULL,
                geomProb=NULL, dirac=NULL, useRootStateMLE=FALSE,
                conditioning=c("oneOrMore", "twoOrMore",
                "oneInBothClades", "none"),
                equalBDrates=FALSE, fixedRetentionRates=TRUE)

`para`	vector of parameters (see Details)
`input`	object output by function `processInput`
`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 evaluated.
`geomProb`	inverse of the prior mean number of gene lineages at the root.
`dirac`	value for the number of genes at the root, when this is assumed to have a fixed value (according to a dirac prior distribution).
`useRootStateMLE`	if `TRUE`, the most likely number of genes at the root is determined for each family separately and is used to evaluate the likelihood function.
`conditioning`	type of conditioning for the likelihood calculation. The default is to calculate conditional probabilities on observing families with at least 1 gene copy (see Details in `MLEGeneCount`).
`equalBDrates`	if `TRUE`, the duplication and loss rates are equal.
`fixedRetentionRates`	if `TRUE`, it uses retention rates present in `input$wgdTab`. If `FALSE`, it uses retention rates in `para`.

The vector para for the parameters to be used is of size 1+number of WGD/Ts if the birth and death rates are assumed equal, or 2+number of WGD/Ts otherwise. It starts with log(StartingBDrates[1]) if equalBDrates is TRUE, with log(StartingBDrates) otherwise. The remaining components correspond to retention rates.

negative log-likelihood value

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.

MLEGeneCount, logLik_CsurosMiklos.

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)
getLikGeneCount(log(c(.01,.02)),a,dat,mMax=8,geomProb=1/1.5,
                conditioning="oneOrMore")