check get_loglik output

[stephens999]

it seems that get_loglik returns penalized likelihood when prior is specified. check if this is desired behaviour.

[esterpantaleo]

ash does not return logLR i.e. if res=ash(...), there is no res$logLR
I have data where this happens:
load("/mnt/lustre/home/epantaleo/src/multiseq/local/testing.pipeline.RData")
library(multiseq) #pull the most recent version
zdat.ash = ash(zdat[3,ind], zdat[4,ind], prior=prior, multiseqoutput=TRUE, pointmass=pointmass, nullcheck=nullcheck, gridmult=gridmult, mixsd=mixsd, VB=VB, onlylogLR=onlylogLR, g=set.fitted.g[[j]])
zdat.ash$logLR
while (using the same loaded data) ash returns logLR:
zdat.rate.ash = ash(zdat.rate[3], zdat.rate[4], prior=prior, pointmass=pointmass, nullcheck=nullcheck, gridmult=gridmult, mixsd=mixsd, VB=VB, onlylogLR=onlylogLR, g=set.fitted.g[[J+1]])
zdat.rate.ash$logLR

[stephens999]

This is a problem with Tom's multiseqoutput flag - it doesn't return logLR when that flag is set.

result = list(fitted.g=pi.fit$g,PosteriorMean = PosteriorMean,PosteriorSD=PosteriorSD,call=match.call())
return(result)