├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── beem2param.r ├── beemDemo.r ├── deprecated.r ├── func.E.r ├── func.EM.r ├── func.M.r ├── normalizations.r ├── post_processing.r └── vis.r ├── README.md ├── README.rmd ├── README_files └── figure-gfm │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-6-1.png ├── beemStatic.Rproj ├── data ├── beemDemo.rda ├── demo.n500_p20_eq1.counts.txt └── demo.n500_p20_eq1.truth.txt ├── logo.png ├── man ├── auc.b.Rd ├── beem2biomass.Rd ├── beem2param.Rd ├── beemDemo.Rd ├── biomassInit.Rd ├── checkPackage.Rd ├── cluster.Rd ├── css.Rd ├── detectDiffModSamples.Rd ├── detectNonEqSamples.Rd ├── diagnoseBiomass.Rd ├── diagnoseFit.Rd ├── entropy.Rd ├── formatOutput.Rd ├── func.E.Rd ├── func.EM.Rd ├── func.M.Rd ├── infer.Rd ├── inference.Rd ├── interaction2association.Rd ├── norm.Rd ├── pcoa.Rd ├── postProcess_perturbation.Rd ├── postProcess_species.Rd ├── preProcess.Rd ├── predict.Rd ├── predict_eq.Rd ├── predict_err.Rd ├── print.Rd ├── resample.EM.Rd ├── showGrowth.Rd ├── showInteraction.Rd └── tss.Rd └── vignettes ├── beem_fit.png ├── beem_param_wo_uncertain.png ├── biomass_compare.png ├── demo.r ├── network.png └── param_compare.png /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lch14forever/beem-static/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lch14forever/beem-static/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lch14forever/beem-static/HEAD/DESCRIPTION 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