cubfits-package	00_cubfits-package
.CF.AC	yy_control
.CF.CONF	yy_control
.CF.CT	yy_control
.CF.DP	yy_control
.CF.GV	yy_control
.CF.OP	yy_control
.CF.PARAM	yy_control
.CF.PT	yy_control
.CO.CT	yy_control
.cubfitsEnv	yy_control
AllDataFormats	xx_dataformat
asl.optim	u4_asl
b	xx_dataformat
b.Init	yy_dataset
bVec	xx_dataformat
calc_cai_values	t4_cai
calc_scuo_values	t2_scuo
calc_scu_values	t5_scu
codon.low2up	u2_convert
codon.up2low	u2_convert
convert.b.to.bVec	u2_convert
convert.bVec.to.b	u2_convert
convert.n.to.list	u2_convert
convert.reu13.df.to.list	u2_convert
convert.seq.data.to.string	u2_convert
convert.y.to.list	u2_convert
convert.y.to.scuo	u2_convert
cp.workflow	zz_internal
cubappr	a2_cubappr
cubfits	a1_cubfits
cubmultichain	c2_convergence
cubpred	a3_cubpred
cubsinglechain	c2_convergence
dasl	u4_asl
dasla	u4_asl
DataConverting	u2_convert
DataGenerating	u1_gen
DataIO	u0_io
dmixnormerr	u5_mixnorm
dna.low2up	u2_convert
dna.up2low	u2_convert
estimatePhi	s2_estimatePhi
ex.test	yy_dataset
ex.train	yy_dataset
fitMultinom	s1_fitMultinom
gen.n	u1_gen
gen.phi.Obs	u1_gen
gen.reu13.df	u1_gen
gen.reu13.list	u1_gen
gen.scuo	u1_gen
gen.y	u1_gen
get.expath	u0_io
get.workflow	zz_internal
init.function	s0_init.function
isConverged	c2_convergence
mixnormerr.optim	u5_mixnorm
n	xx_dataformat
n.list	xx_dataformat
normalizeDataSet	c1_io
pasl	u4_asl
pasla	u4_asl
phi.df	xx_dataformat
phi.Obs	xx_dataformat
plotaddmodel	b2_plotmodel
plotbin	b1_plotbin
plotbin.NSE	c9_internal
plotBMatrixPosterior	c9_internal
plotCUB	c0_plot
plotCUB.NSE	c9_internal
plotExpectedPhiTrace	c0_plot
plotmodel	b2_plotmodel
plotprxy	b0_plotprxy
plotPTraces	c0_plot
plotTraces	c0_plot
print.mixnormerr	vv_print
prop.bin.roc	b1_plotbin
prop.model.nse	c9_internal
prop.model.roc	b2_plotmodel
qasl	u4_asl
qasla	u4_asl
rasl	u4_asl
rasla	u4_asl
read.phi.df	u0_io
read.seq	u0_io
readGenome	c1_io
rearrange.n	u3_rearrange
rearrange.phi.Obs	u3_rearrange
rearrange.reu13.df	u3_rearrange
rearrange.y	u3_rearrange
reu13.df	xx_dataformat
reu13.list	xx_dataformat
scuo	xx_dataformat
scuo.random	t3_scuo.random
seq.data	xx_dataformat
seq.string	xx_dataformat
simu.mixnormerr	t1_simulation
simu.orf	t1_simulation
simu.phi.Obs	t1_simulation
write.phi.df	u0_io
write.seq	u0_io
y	xx_dataformat
y.list	xx_dataformat
yassour	yy_yassour
yassour.info	yy_yassour_PM
yassour.PM.appr	yy_yassour_PM
yassour.PM.fits	yy_yassour_PM
