├── .gitignore ├── ALDEx2 ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R │ ├── AllClasses.R │ ├── AllGenerics.R │ ├── aldex.r │ ├── clr_corr.R │ ├── clr_effect.r │ ├── clr_function.r │ ├── clr_glm.r │ ├── clr_ttest.r │ ├── iqlr_features.r │ ├── plot.aldex.r │ ├── progress.R │ ├── rdirichlet.r │ └── stats.fast.R ├── data │ └── selex.txt.gz ├── inst │ └── CITATION ├── man │ ├── ALDEx2m-package.Rd │ ├── aldex.Rd │ ├── aldex.clr-class.Rd │ ├── aldex.clr.function-methods.Rd │ ├── aldex.corr.Rd │ ├── aldex.effect.Rd │ ├── aldex.glm.Rd │ ├── aldex.set.mode.Rd │ ├── aldex.ttest.Rd │ ├── getFeatureNames-method.Rd │ ├── getFeatures-method.Rd │ ├── getMonteCarloInstances-method.Rd │ ├── getMonteCarloReplicate-method.Rd │ ├── getReads-method.Rd │ ├── getSampleIDs-method.Rd │ ├── numConditions-method.Rd │ ├── numFeatures-method.Rd │ ├── numMCInstances-method.Rd │ ├── plot.aldex.Rd │ └── selex.Rd ├── tests │ ├── testthat.R │ └── testthat │ │ ├── test-aldex.glm.R │ │ ├── test-aldex.ttest.R │ │ └── test-stats.fast.R └── vignettes │ └── ALDEx2_vignette.Rnw ├── ALDEx2_1.6.1.tar.gz ├── ALDEx2_1.6.2.tar.gz ├── ALDEx2_1.6.3.tar.gz ├── ALDEx2_1.8.1.tar.gz ├── ALDEx2_1.9.1.tar.gz ├── ALDEx2_1.9.3.tar.gz ├── Development ├── ALDEx2_0.99.1.tar.gz ├── ALDEx2_0.99.2.tar.gz └── ALDEx_1.0.4.tar.gz ├── LICENSE ├── README.md ├── SumFunctionsAitchison.R ├── kendalls_tau_working.R ├── manual ├── ALDEX_manual_modular_2.0.aux ├── ALDEX_manual_modular_2.0.bbl ├── ALDEX_manual_modular_2.0.blg ├── ALDEX_manual_modular_2.0.log ├── ALDEX_manual_modular_2.0.pdf ├── ALDEX_manual_modular_2.0.synctex.gz ├── ALDEX_manual_modular_2.0.tex ├── ALDEX_manual_modular_2.0.toc ├── ALDEX_manual_tex_2.0.aux ├── ALDEX_manual_tex_2.0.bbl ├── ALDEX_manual_tex_2.0.blg ├── ALDEX_manual_tex_2.0.dvi ├── ALDEX_manual_tex_2.0.log ├── ALDEX_manual_tex_2.0.pdf ├── ALDEX_manual_tex_2.0.tex ├── ALDEX_manual_tex_2.0.toc ├── ALDEx2_manual.Rnw ├── ALDEx2_manual.pdf ├── ALDEx2_vignette.pdf ├── DirvsBH.pdf ├── aldex_plot.pdf ├── bottomly.pdf ├── effect.pdf ├── selex_comparison.pdf ├── selex_mw.pdf └── selex_venn.png ├── sd_vs_diff.win.R └── t_test_aitchison.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/.gitignore -------------------------------------------------------------------------------- /ALDEx2/DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/DESCRIPTION -------------------------------------------------------------------------------- /ALDEx2/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/LICENSE -------------------------------------------------------------------------------- /ALDEx2/NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/NAMESPACE -------------------------------------------------------------------------------- /ALDEx2/NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/NEWS -------------------------------------------------------------------------------- /ALDEx2/R/AllClasses.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/AllClasses.R -------------------------------------------------------------------------------- /ALDEx2/R/AllGenerics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/AllGenerics.R -------------------------------------------------------------------------------- /ALDEx2/R/aldex.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/aldex.r -------------------------------------------------------------------------------- /ALDEx2/R/clr_corr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/clr_corr.R -------------------------------------------------------------------------------- /ALDEx2/R/clr_effect.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/clr_effect.r -------------------------------------------------------------------------------- /ALDEx2/R/clr_function.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/clr_function.r -------------------------------------------------------------------------------- /ALDEx2/R/clr_glm.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/clr_glm.r -------------------------------------------------------------------------------- /ALDEx2/R/clr_ttest.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/clr_ttest.r -------------------------------------------------------------------------------- /ALDEx2/R/iqlr_features.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/iqlr_features.r -------------------------------------------------------------------------------- /ALDEx2/R/plot.aldex.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/plot.aldex.r -------------------------------------------------------------------------------- /ALDEx2/R/progress.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/progress.R -------------------------------------------------------------------------------- /ALDEx2/R/rdirichlet.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/rdirichlet.r -------------------------------------------------------------------------------- /ALDEx2/R/stats.fast.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/R/stats.fast.R -------------------------------------------------------------------------------- /ALDEx2/data/selex.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/data/selex.txt.gz -------------------------------------------------------------------------------- /ALDEx2/inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/inst/CITATION -------------------------------------------------------------------------------- /ALDEx2/man/ALDEx2m-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/ALDEx2m-package.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.clr-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.clr-class.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.clr.function-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.clr.function-methods.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.corr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.corr.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.effect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.effect.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.glm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.glm.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.set.mode.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.set.mode.Rd -------------------------------------------------------------------------------- /ALDEx2/man/aldex.ttest.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/aldex.ttest.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getFeatureNames-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getFeatureNames-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getFeatures-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getFeatures-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getMonteCarloInstances-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getMonteCarloInstances-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getMonteCarloReplicate-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getMonteCarloReplicate-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getReads-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getReads-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/getSampleIDs-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/getSampleIDs-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/numConditions-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/numConditions-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/numFeatures-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/numFeatures-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/numMCInstances-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/numMCInstances-method.Rd -------------------------------------------------------------------------------- /ALDEx2/man/plot.aldex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/plot.aldex.Rd -------------------------------------------------------------------------------- /ALDEx2/man/selex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/man/selex.Rd -------------------------------------------------------------------------------- /ALDEx2/tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/tests/testthat.R -------------------------------------------------------------------------------- /ALDEx2/tests/testthat/test-aldex.glm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/tests/testthat/test-aldex.glm.R -------------------------------------------------------------------------------- /ALDEx2/tests/testthat/test-aldex.ttest.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/tests/testthat/test-aldex.ttest.R -------------------------------------------------------------------------------- /ALDEx2/tests/testthat/test-stats.fast.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/tests/testthat/test-stats.fast.R -------------------------------------------------------------------------------- /ALDEx2/vignettes/ALDEx2_vignette.Rnw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2/vignettes/ALDEx2_vignette.Rnw -------------------------------------------------------------------------------- /ALDEx2_1.6.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.6.1.tar.gz -------------------------------------------------------------------------------- /ALDEx2_1.6.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.6.2.tar.gz -------------------------------------------------------------------------------- /ALDEx2_1.6.3.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.6.3.tar.gz -------------------------------------------------------------------------------- /ALDEx2_1.8.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.8.1.tar.gz -------------------------------------------------------------------------------- /ALDEx2_1.9.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.9.1.tar.gz -------------------------------------------------------------------------------- /ALDEx2_1.9.3.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/ALDEx2_1.9.3.tar.gz -------------------------------------------------------------------------------- /Development/ALDEx2_0.99.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/Development/ALDEx2_0.99.1.tar.gz -------------------------------------------------------------------------------- /Development/ALDEx2_0.99.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/Development/ALDEx2_0.99.2.tar.gz -------------------------------------------------------------------------------- /Development/ALDEx_1.0.4.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/Development/ALDEx_1.0.4.tar.gz -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/README.md -------------------------------------------------------------------------------- /SumFunctionsAitchison.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/SumFunctionsAitchison.R -------------------------------------------------------------------------------- /kendalls_tau_working.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/kendalls_tau_working.R -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.aux: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.aux -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.bbl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.bbl -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.blg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.blg -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.log -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.pdf -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.synctex.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.synctex.gz -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.tex -------------------------------------------------------------------------------- /manual/ALDEX_manual_modular_2.0.toc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_modular_2.0.toc -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.aux: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.aux -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.bbl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.bbl -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.blg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.blg -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.dvi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.dvi -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.log -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.pdf -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.tex -------------------------------------------------------------------------------- /manual/ALDEX_manual_tex_2.0.toc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEX_manual_tex_2.0.toc -------------------------------------------------------------------------------- /manual/ALDEx2_manual.Rnw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEx2_manual.Rnw -------------------------------------------------------------------------------- /manual/ALDEx2_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEx2_manual.pdf -------------------------------------------------------------------------------- /manual/ALDEx2_vignette.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/ALDEx2_vignette.pdf -------------------------------------------------------------------------------- /manual/DirvsBH.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/DirvsBH.pdf -------------------------------------------------------------------------------- /manual/aldex_plot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/aldex_plot.pdf -------------------------------------------------------------------------------- /manual/bottomly.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/bottomly.pdf -------------------------------------------------------------------------------- /manual/effect.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/effect.pdf -------------------------------------------------------------------------------- /manual/selex_comparison.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/selex_comparison.pdf -------------------------------------------------------------------------------- /manual/selex_mw.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/selex_mw.pdf -------------------------------------------------------------------------------- /manual/selex_venn.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/manual/selex_venn.png -------------------------------------------------------------------------------- /sd_vs_diff.win.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/sd_vs_diff.win.R -------------------------------------------------------------------------------- /t_test_aitchison.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ggloor/ALDEx2_dev/HEAD/t_test_aitchison.R --------------------------------------------------------------------------------