### - PM method will return the phi * L * 1 for given phi
### These are only called by the integrate function to find the posterior
### mean.
### - These functions are based on per gene list in the following order
### genes -> amino acids -> synonymous codons -> counts
### for reu13.list.g, y.g, and n.g.
### - add.llv.g is to scale log likelihood value for a gene.
### Return x * Likelihood(phi) * flat prior
### For ROC + NSEf model.
my.objectivePhiOne.xLfp.rocnsef <- function(phi, fitlist, reu13.list.g, y.g,
n.g, add.llv.g = 0.0){
ret <- my.objectivePhiOne.nlogL.rocnsef(phi, fitlist, reu13.list.g, y.g, n.g)
ret <- exp(-ret + log(phi) + add.llv.g)
ret
} # End of my.objectivePhiOne.xLfp.rocnsef().
### For ROC model.
my.objectivePhiOne.xLfp.roc <- function(phi, fitlist, reu13.list.g, y.g, n.g,
add.llv.g = 0.0){
ret <- my.objectivePhiOne.nlogL.roc(phi, fitlist, reu13.list.g, y.g, n.g)
ret <- exp(-ret + log(phi) + add.llv.g)
ret
} # End of my.objectivePhiOne.xLfp.roc().
### For NSEf model.
my.objectivePhiOne.xLfp.nsef <- function(phi, fitlist, reu13.list.g, y.g, n.g,
add.llv.g = 0.0){
ret <- my.objectivePhiOne.nlogL.nsef(phi, fitlist, reu13.list.g, y.g, n.g)
ret <- exp(-ret + log(phi) + add.llv.g)
ret
} # End of my.objectivePhiOne.xLfp.nsef().
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