API for snoweye/cubfits
Codon Usage Bias Fits

Global functions
.CF.AC Man page
.CF.CONF Man page
.CF.CT Man page
.CF.DP Man page
.CF.GV Man page
.CF.OP Man page
.CF.PARAM Man page
.CF.PT Man page
.CO.CT Man page
.cubfitsEnv Man page
AllDataFormats Man page
DataConverting Man page
DataGenerating Man page
DataIO Man page
appendCUBresults Source code
asl.alpha.beta Source code
asl.logL Source code
asl.optim Man page Source code
asl.optim.init Source code
b Man page
b.Init Man page
bVec Man page
build.aa.df Source code
build.n Source code
build.reu13.df Source code
build.reu13.list Source code
build.scuo Source code
build.y Source code
calc_cai_values Man page Source code
calc_scu_values Man page Source code
calc_scuo_values Man page Source code
codon.low2up Man page Source code
codon.up2low Man page Source code
codon2string Source code
convert.b.to.bVec Man page Source code
convert.bVec.to.b Man page Source code
convert.n.to.list Man page Source code
convert.reu13.df.to.list Man page Source code
convert.seq.data.to.string Man page Source code
convert.y.to.list Man page Source code
convert.y.to.scuo Man page Source code
cp.workflow Man page Source code
cubappr Man page
cubfits Man page
cubfits-package Man page
cubmultichain Man page Source code
cubpred Man page
cubsinglechain Man page Source code
dasl Man page Source code
dasla Man page Source code
dasla.one.log Source code
ddirichlet Source code
dlmixnorm Source code
dmixnorm Source code
dmixnormerr Man page Source code
dmixnormerr.one Source code
dna.low2up Man page Source code
dna.up2low Man page Source code
estimatePhi Man page Source code
ex.test Man page
ex.train Man page
find.prop Source code
find.prop.bin.roc Source code
find.prop.model.nse Source code
find.prop.model.roc Source code
fitMultinom Man page Source code
gen.n Man page Source code
gen.phi.Obs Man page Source code
gen.reu13.df Man page Source code
gen.reu13.list Man page Source code
gen.scuo Man page Source code
gen.y Man page Source code
get.color Source code
get.expath Man page Source code
get.my.cat Source code
get.my.coefnames Source code
get.my.drawBConditionalAll Source code
get.my.dump Source code
get.my.estimatePhiAll Source code
get.my.estimatePhiOne Source code
get.my.fitMultinomAll Source code
get.my.fitMultinomOne Source code
get.my.logLAll Source code
get.my.logLAllPred Source code
get.my.logPosteriorAll Source code
get.my.logPosteriorAllPred Source code
get.my.logdmultinomCodAllR Source code
get.my.logdmultinomCodOne Source code
get.my.ncoef Source code
get.my.pPropType Source code
get.my.pPropTypeNoObs Source code
get.my.print Source code
get.my.proposePhiAll Source code
get.my.proposePhiAllPred Source code
get.my.stop Source code
get.my.update.DrawScale Source code
get.param Source code
get.workflow Man page Source code
getBInitFromSwapBMat Source code
h.theta Source code
init.function Man page
init.param Source code
isConverged Man page Source code
mapBMatNames Source code
mixnormerr.nlogL Source code
mixnormerr.optim Man page Source code
my.DrawScale.scaling Source code
my.cat.lapply Source code
my.cat.pbdLapply Source code
my.cat.task.pull Source code
my.check.acceptance Source code
my.check.data Source code
my.check.rearrange Source code
my.copy.adaptive Source code
my.cubappr Source code
my.cubfits Source code
my.cubpred Source code
my.drawBConditionalAll.RW_Norm Source code
my.drawBConditionalAll.current Source code
my.drawBConditionalAll.random Source code
my.drawBConditionalFit.ID_Norm Source code
my.drawBConditionalFit.MH Source code
my.drawBConditionalFit.RW_Norm Source code
my.drawBPrior Source code
my.drawPhiConditionalAll Source code
my.drawPhiConditionalAllPred Source code
my.drawRestrictHP Source code
my.drawSPhiPrior Source code
my.drawbiasPhi Source code
my.dump.lapply Source code
my.dump.pbdLapply Source code
my.dump.task.pull Source code
my.estimatePhiAll.lapply Source code
my.estimatePhiAll.mclapply Source code
my.estimatePhiAll.pbdLapply Source code
my.estimatePhiAll.task.pull Source code
my.estimatePhiOne.MLE.nsef Source code
my.estimatePhiOne.MLE.roc Source code
my.estimatePhiOne.MLE.rocnsef Source code
my.estimatePhiOne.PM.nsef Source code
my.estimatePhiOne.PM.roc Source code
my.estimatePhiOne.PM.rocnsef Source code
my.fitMultinomAll.lapply Source code
my.fitMultinomAll.mclapply Source code
my.fitMultinomAll.pbdLapply Source code
my.fitMultinomAll.task.pull Source code
my.fitMultinomOne.nsef Source code
my.fitMultinomOne.roc Source code
my.fitMultinomOne.rocnsef Source code
my.format Source code
my.generate.list Source code
my.init.function Source code
my.integrate Source code
my.inverse.mlogit Source code
my.logLAll.logmixture Source code
my.logLAll.lognormal Source code
my.logLAllPred.logmixture Source code
my.logLAllPred.lognormal Source code
my.logPosteriorAll.logmixture Source code
my.logPosteriorAll.logmixture_bias Source code
my.logPosteriorAll.lognormal Source code
my.logPosteriorAll.lognormal_bias Source code
my.logPosteriorAllPred.logmixture Source code
my.logPosteriorAllPred.lognormal Source code
my.logdmultinomCodAllR.lapply Source code
my.logdmultinomCodAllR.mclapply Source code
my.logdmultinomCodAllR.pbdLapply Source code
my.logdmultinomCodAllR.task.pull Source code
my.logdmultinomCodOne.nsef Source code
my.logdmultinomCodOne.roc Source code
my.logdmultinomCodOne.rocnsef Source code
my.objectivePhiOne.Lfp.nsef Source code
my.objectivePhiOne.Lfp.roc Source code
my.objectivePhiOne.Lfp.rocnsef Source code
my.objectivePhiOne.nlogL.nsef Source code
my.objectivePhiOne.nlogL.roc Source code
my.objectivePhiOne.nlogL.rocnsef Source code
my.objectivePhiOne.nlogphiL.nsef Source code
my.objectivePhiOne.nlogphiL.roc Source code
my.objectivePhiOne.nlogphiL.rocnsef Source code
my.objectivePhiOne.xLfp.nsef Source code
my.objectivePhiOne.xLfp.roc Source code
my.objectivePhiOne.xLfp.rocnsef Source code
my.pInit Source code
my.pPropType.logmixture Source code
my.pPropType.lognormal_RW Source code
my.pPropType.lognormal_bias Source code
my.pPropType.lognormal_fix Source code
my.pPropTypeNoObs.logmixture Source code
my.pPropTypeNoObs.lognormal_RW Source code
my.pPropTypeNoObs.lognormal_bias Source code
my.pPropTypeNoObs.lognormal_fix Source code
my.print.lapply Source code
my.print.pbdLapply Source code
my.print.task.pull Source code
my.propose.paramlog Source code
my.proposeB.ID_Norm Source code
my.proposeB.RW_Norm Source code
my.proposePhiAll.RW_Norm Source code
my.proposePhiAllPred.RW_Norm Source code
my.proposebiasPhi.RW_Norm Source code
my.proposesigmaPhi.RW_Norm Source code
my.set.acceptance Source code
my.set.adaptive Source code
my.stop.lapply Source code
my.stop.pbdLapply Source code
my.stop.task.pull Source code
my.update.DrawScale.none Source code
my.update.DrawScale.simple Source code
my.update.acceptance Source code
my.update.adaptive Source code
my.verbose Source code
n Man page
n.list Man page
normalizeDataSet Man page Source code
onAttach Source code
onLoad Source code
onUnload Source code
oneLetterAAtoThreeLetterAA Source code
optim.mixnormerr.logL Source code
pasl Man page Source code
pasla Man page Source code
pasla.one.log Source code
phi.Obs Man page
phi.df Man page
plotBMatrixPosterior Man page Source code
plotCUB Man page Source code
plotCUB.NSE Man page Source code
plotExpectedPhiTrace Man page Source code
plotPTraces Man page Source code
plotTraces Man page Source code
plotaddmodel Man page Source code
plotbin Man page Source code
plotbin.NSE Man page Source code
plotmodel Man page Source code
plotprxy Man page Source code
print.mixnormerr Man page Source code
prop.bin.roc Man page Source code
prop.model.nse Man page Source code
prop.model.roc Man page Source code
proplmixnorm Source code
qasl Man page Source code
qasla Man page Source code
qasla.one.log Source code
rasl Man page Source code
rasla Man page Source code
rdirichlet Source code
read.phi.df Man page Source code
read.seq Man page Source code
readGenome Man page Source code
rearrange.n Man page Source code
rearrange.phi.Obs Man page Source code
rearrange.reu13.df Man page Source code
rearrange.y Man page Source code
reu13.df Man page
reu13.list Man page
scuo Man page
scuo.random Man page Source code
seq.data Man page
seq.string Man page
simu.mixnormerr Man page Source code
simu.orf Man page Source code
simu.orf.nsef Source code
simu.orf.roc Source code
simu.orf.rocnsef Source code
simu.phi.Obs Man page Source code
write.phi.df Man page Source code
write.seq Man page Source code
y Man page
y.list Man page
yassour Man page
yassour.PM.appr Man page
yassour.PM.fits Man page
yassour.info Man page
snoweye/cubfits documentation built on May 26, 2017, 1:28 p.m.