Files in snoweye/cubfits
Codon Usage Bias Fits

.gitignore

COPYING

ChangeLog

DESCRIPTION

INSTALL

NAMESPACE

R/000_globalVariables.r R/asl.density.r R/asl.optim.r R/asl.probability.r R/asl.quantile.r R/asl.random.r R/cedric.convergence.r R/cedric.io.r R/cedric.mapBMatNames.r R/cedric.plotting.r R/data.codon.convert.r R/data.convert.r R/data.gen.n.r R/data.gen.phi.Obs.r R/data.gen.reu13.df.r R/data.gen.reu13.list.r R/data.gen.y.r R/data.io.r R/data.rearrange.r R/dsn.dirichlet.r R/dsn.logmixture.r R/index.cai.r R/index.gen.scuo.r R/index.scu.r R/index.scuo.r R/index.scuo.random.r R/logan.plotting.r R/mixnormerr.optim.r R/my.acceptance.r R/my.adaptive.DrawScale.r R/my.adaptive.r R/my.cat.r R/my.check.data.r R/my.check.rearrange.r R/my.coef.r R/my.cubappr.r R/my.cubfits.r R/my.cubpred.r R/my.drawBConditionalAll.r R/my.drawBConditionalFit.r R/my.drawPhiConditionalAll.r R/my.drawPhiConditionalAllPred.r R/my.drawRestrictHP.r R/my.drawbiasPhi.r R/my.dump.r R/my.estimatePhiAll.r R/my.estimatePhiOne.r R/my.fitMultinomAll.r R/my.fitMultinomOne.r R/my.init.r R/my.init_param.r R/my.inverse.mlogit.r R/my.logLAll.r R/my.logLAllPred.r R/my.logPosteriorAll.r R/my.logPosteriorAllPred.r R/my.logdmultinomCodAll.r R/my.logdmultinomCodOne.r R/my.objectivePhiOne.Lfp.r R/my.objectivePhiOne.nlogL.r R/my.objectivePhiOne.nlogphiL.r R/my.objectivePhiOne.phiLfp.r R/my.pPropType.logmixture.r R/my.pPropType.lognormal_RW.r R/my.pPropType.lognormal_bias.r R/my.pPropType.r R/my.pPropTypeNoObs.logmixture.r R/my.pPropTypeNoObs.lognormal_RW.r R/my.pPropTypeNoObs.lognormal_bias.r R/my.pPropTypeNoObs.r R/my.print.r R/my.proposeB.r R/my.proposePhiAll.r R/my.proposePhiAllPred.r R/my.proposebiasPhi.r R/my.proposesigmaPhi.r R/my.stop.r R/my.util.r R/my.verbose.r R/plotbin.r R/plotcolor.r R/plotmodel.r R/plotprxy.r R/prop.bin.roc.r R/prop.model.nse.r R/prop.model.roc.r R/simu.mixnormerr.r R/simu.orf.r R/simu.phi.Obs.r R/workflow.create.r R/workflow.get.expath.r R/yyy.r R/zzz.r

README

cleanup

configure

configure.ac

configure.win

data/b.Init.rda

data/control.r data/control_optim.r data/envir.r

data/ex.test.rda

data/ex.train.rda

data/global.r data/plot.r

data/yassour.mcmc.rda

data/yassour.rda

demo/00Index

demo/basic.r demo/cai.r demo/fitMultinom.r demo/mSCU.r demo/plotbin.r demo/roc.appr.r demo/roc.pred.r demo/roc.simu.r demo/roc.train.r demo/scuo.r demo/yassour.asl.r demo/yassour.mixed.r demo/yassour.mixture.r

inst/CITATION

inst/doc/cubfits-guide.Rnw

inst/doc/cubfits-guide.pdf

inst/ex_data/phi_200.tsv

inst/ex_data/seq_200.fasta

inst/workflow/00_readme.txt

inst/workflow/param/small_bInit.rda

inst/workflow/param/small_length.rda

inst/workflow/param/small_train.rda

inst/workflow/roc/00_readme.txt

inst/workflow/roc/01_code.txt

inst/workflow/roc/script/simu_run_0.sh

inst/workflow/roc/script/simu_run_1.sh

inst/workflow/roc/script/simu_run_2.sh

inst/workflow/roc/script/simu_run_2_ps.sh

inst/workflow/roc/script/wophi_run_0.sh

inst/workflow/roc/script/wophi_run_1.sh

inst/workflow/roc/script/wophi_run_2.sh

inst/workflow/roc/script/wophi_run_2_ps.sh

inst/workflow/roc/script/wphi_run_0.sh

inst/workflow/roc/script/wphi_run_1.sh

inst/workflow/roc/script/wphi_run_2.sh

inst/workflow/roc/script/wphi_run_2_ps.sh

inst/workflow/roc/script/wphi_wophi_run_0.sh

inst/workflow/roc/script/wphi_wophi_run_1.sh

inst/workflow/roc/script/wphi_wophi_run_2.sh

inst/workflow/roc/script/wphi_wophi_run_2_ps.sh

man/00_cubfits-package.Rd man/a1_cubfits.Rd man/a2_cubappr.Rd man/a3_cubpred.Rd man/b0_plotprxy.Rd man/b1_plotbin.Rd man/b2_plotmodel.Rd man/c0_plot.Rd man/c1_io.Rd man/c2_convergence.Rd man/c9_internal.Rd man/s0_init.function.Rd man/s1_fitMultinom.Rd man/s2_estimatePhi.Rd man/t1_simulation.Rd man/t2_scuo.Rd man/t3_scuo.random.Rd man/t4_cai.Rd man/t5_scu.Rd man/u0_io.Rd man/u1_gen.Rd man/u2_convert.Rd man/u3_rearrange.Rd man/u4_asl.Rd man/u5_mixnorm.Rd man/vv_print.Rd man/xx_dataformat.Rd man/yy_control.Rd man/yy_dataset.Rd man/yy_yassour.Rd man/yy_yassour_PM.Rd man/zz_internal.Rd

src/Makevars.in

src/Makevars.win

src/lib.c

src/lp_c_raw.c

src/stable_exp.c

src/zzz.c

src/zzz.h

vignettes/build_pdf.sh

vignettes/cubfits-guide.Rnw

vignettes/cubfits-include/00-preamble.tex

vignettes/cubfits-include/01-acknowledgement.tex

vignettes/cubfits-include/01-copyright.tex

vignettes/cubfits-include/01-introduction.tex

vignettes/cubfits-include/02-main_functions.tex

vignettes/cubfits-include/03-speedup.tex

vignettes/cubfits-include/04-workflows.tex

vignettes/cubfits-include/05-utilities.tex

vignettes/cubfits-include/06-faq.tex

vignettes/cubfits-include/07-misc.tex

vignettes/cubfits-include/cubfits.bib

vignettes/cubfits-include/figure/avg_run_time.pdf vignettes/cubfits-include/figure/bayesian_model.pdf vignettes/cubfits-include/figure/fitMultinom.pdf vignettes/cubfits-include/figure/more_asl.pdf vignettes/cubfits-include/figure/more_mixture.pdf vignettes/cubfits-include/figure/plotbin.pdf vignettes/cubfits-include/figure/prxy_roc_ad_appr_pm_5k-10k.pdf vignettes/cubfits-include/figure/prxy_roc_ad_fits_pm_5k-10k.pdf vignettes/cubfits-include/figure/workflows.pdf

vignettes/cubfits-include/my_jss.cls

snoweye/cubfits documentation built on Nov. 9, 2021, 3:39 a.m.

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snoweye/cubfits
Codon Usage Bias Fits

Files in snoweye/cubfits
Codon Usage Bias Fits

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snoweye/cubfits Codon Usage Bias Fits

Files in snoweye/cubfits Codon Usage Bias Fits

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snoweye/cubfits
Codon Usage Bias Fits

Files in snoweye/cubfits
Codon Usage Bias Fits