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/code/00-set_env_simu.r inst/workflow/roc/code/00-set_env_wophi.r inst/workflow/roc/code/00-set_env_wphi.r inst/workflow/roc/code/00-set_env_wphi_wophi.r inst/workflow/roc/code/01-mkdir_output.r inst/workflow/roc/code/02-get_data.r inst/workflow/roc/code/03-get_init-tp.r inst/workflow/roc/code/04-wophi_pm-tp.r inst/workflow/roc/code/04-wophi_scuo-tp.r inst/workflow/roc/code/04-wphi_pm-tp.r inst/workflow/roc/code/04-wphi_scuo-tp.r inst/workflow/roc/code/04-wphi_wophi_pm-tp.r inst/workflow/roc/code/04-wphi_wophi_scuo-tp.r inst/workflow/roc/code/05-subset-tp.r inst/workflow/roc/code/s1-generate_data.r inst/workflow/roc/code/s4-wophi_true-tp.r inst/workflow/roc/code/s4-wphi_true-tp.r inst/workflow/roc/code/u1-get_negsel.r inst/workflow/roc/code_plot/03-plotdiag_bin_est.r inst/workflow/roc/code_plot/03-plotdiag_init.r inst/workflow/roc/code_plot/05-subset_tsv.r inst/workflow/roc/code_plot/06-plotsingle_model.r inst/workflow/roc/code_plot/06-plotsingle_prxy.r inst/workflow/roc/code_plot/06-plotsingle_prxy_wci.r inst/workflow/roc/code_plot/07-plotdiag_EPhi_hist.r inst/workflow/roc/code_plot/07-plotdiag_accept_hist.r inst/workflow/roc/code_plot/07-plotdiag_acceptvsEPhi.r inst/workflow/roc/code_plot/07-plotdiag_bin.r inst/workflow/roc/code_plot/07-plotdiag_medPhi_EPhi.r inst/workflow/roc/code_plot/07-plotdiag_scuo_cai.r inst/workflow/roc/code_plot/07-plotdiag_sigmaW_hist.r inst/workflow/roc/code_plot/07-plottrace_logL-tp.r inst/workflow/roc/code_plot/07-plottrace_param_meanEPhi.r inst/workflow/roc/code_plot/07-plottrace_prior.r inst/workflow/roc/code_plot/07-plottrace_quantile_Phi.r inst/workflow/roc/code_plot/08-plotmulti_wophi_wphi.r inst/workflow/roc/code_plot/m6-plot_b_corr.r inst/workflow/roc/code_plot/m6-plot_b_corr_negsel.r inst/workflow/roc/code_plot/m6-plot_prxy.r inst/workflow/roc/code_plot/m6-plot_prxy_wci.r inst/workflow/roc/code_plot/m7-plot_bin.r inst/workflow/roc/code_plot/s1-plotdiag_simu_phi.r inst/workflow/roc/code_plot/s2-plotdiag_bin_true.r inst/workflow/roc/code_plot/s3-plotdiag_bin_est.r inst/workflow/roc/code_plot/s6-plotsingle_b_corr_true.r inst/workflow/roc/code_plot/s6-plotsingle_model_true.r inst/workflow/roc/code_plot/s6-plotsingle_mscu.r inst/workflow/roc/code_plot/s6-plotsingle_prxy_true.r inst/workflow/roc/code_plot/s6-plotsingle_prxy_true_wci.r inst/workflow/roc/code_plot/s6-plotsingle_scu_mscu.r inst/workflow/roc/code_plot/s7-plotaa_deltat_true.r inst/workflow/roc/code_plot/s8-plotmulti_true.r inst/workflow/roc/code_plot/u0-get_case_main.r inst/workflow/roc/code_plot/u2-plot_b_corr.r inst/workflow/roc/code_plot/u3-plot_trace.r inst/workflow/roc/code_plot/u4-plot_aa_allinone.r inst/workflow/roc/code_plot/u5-new_page.r inst/workflow/roc/code_plot/u6-adjust_focal_codon.r inst/workflow/roc/code_plot_ps/05-subset_tsv.r inst/workflow/roc/code_plot_ps/06-plotsingle_model.r inst/workflow/roc/code_plot_ps/06-plotsingle_prxy.r inst/workflow/roc/code_plot_ps/06-plotsingle_prxy_wci.r inst/workflow/roc/code_plot_ps/07-plotdiag_EPhi_hist.r inst/workflow/roc/code_plot_ps/07-plotdiag_acceptvsEPhi.r inst/workflow/roc/code_plot_ps/07-plotdiag_bin.r inst/workflow/roc/code_plot_ps/07-plottrace_logL-tp.r inst/workflow/roc/code_plot_ps/07-plottrace_quantile_Phi.r inst/workflow/roc/code_plot_ps/08-plotmulti_wophi_wphi.r inst/workflow/roc/code_plot_ps/m6-plot_b_corr.r inst/workflow/roc/code_plot_ps/m6-plot_b_corr_negsel.r inst/workflow/roc/code_plot_ps/m6-plot_prxy.r inst/workflow/roc/code_plot_ps/m6-plot_prxy_wci.r inst/workflow/roc/code_plot_ps/m7-plot_bin.r inst/workflow/roc/code_plot_ps/s6-plotsingle_b_corr_true.r inst/workflow/roc/code_plot_ps/s6-plotsingle_model_true.r inst/workflow/roc/code_plot_ps/s6-plotsingle_mscu.r inst/workflow/roc/code_plot_ps/s6-plotsingle_prxy_true.r inst/workflow/roc/code_plot_ps/s6-plotsingle_prxy_true_wci.r inst/workflow/roc/code_plot_ps/s6-plotsingle_scu_mscu.r inst/workflow/roc/code_plot_ps/s7-plotaa_deltat_true.r inst/workflow/roc/code_plot_ps/s8-plotmulti_true.r inst/workflow/roc/code_plot_ps/u0-get_case_main.r inst/workflow/roc/code_plot_ps/u2-plot_b_corr.r inst/workflow/roc/code_plot_ps/u3-plot_trace.r inst/workflow/roc/code_plot_ps/u4-plot_aa_allinone.r inst/workflow/roc/code_plot_ps/u5-new_page.r inst/workflow/roc/code_plot_ps/u6-adjust_focal_codon.r
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/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 May 26, 2017, 1:28 p.m.