PratheepaJ/diffTop
Differential topic analysis using latent Dirichlet allocation

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Differential topic analysis using latent Dirichlet allocation

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/LDAtopicmodel.R R/alignmentMatrix.R R/betaAligned.R R/dds_all_K_11.R R/dds_all_paired_K_11.R R/dds_all_paired_aster_K_11.R R/dds_all_paired_nonaster_K_11.R R/diagnosticsPlot.R R/diffTop-package.R R/diffTopAnalysis.R R/modelAssessment.R R/phyloseqTransformation.R R/plotASVCircular.R R/plotTopicProportion.R R/powerstand.R R/powerswitch.R R/psE.R R/psE_BARBI.R R/ps_ans.R R/setUpData.R R/stanmodels.R R/thetaAligned.R R/writeResTable.R
_pkgdown.yml
configure
configure.win
data/dds_all_K_11.rda
data/dds_all_paired_K_11.rda
data/dds_all_paired_aster_K_11.rda
data/dds_all_paired_nonaster_K_11.rda
data/powerstand.rda
data/powerswitch.rda
data/psE.rda
data/psE_BARBI.rda
data/ps_ans.rda
diffTop.Rproj
docs/404.html
docs/articles/appendix/01_introduction.html
docs/articles/appendix/01_introduction_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/02_microbiome_data.html
docs/articles/appendix/02_microbiome_data_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/03_example_16S_data.html
docs/articles/appendix/03_example_16S_data_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/04_models.html
docs/articles/appendix/04_models_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/05_transformation.html
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-10-1.png
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-11-1.png
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-13-1.png
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-15-1.png
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-8-1.png
docs/articles/appendix/05_transformation_files/figure-html/unnamed-chunk-9-1.png
docs/articles/appendix/05_transformation_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/06_visualization.html
docs/articles/appendix/06_visualization_files/figure-html/unnamed-chunk-11-1.png
docs/articles/appendix/06_visualization_files/figure-html/unnamed-chunk-13-1.png
docs/articles/appendix/06_visualization_files/figure-html/unnamed-chunk-14-1.png
docs/articles/appendix/06_visualization_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/07_multivariate_and_network_analysis.html
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-10-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-11-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-12-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-13-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-15-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-7-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-8-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-9-1.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/figure-html/unnamed-chunk-9-2.png
docs/articles/appendix/07_multivariate_and_network_analysis_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/08_differential_abundance_analysis.html
docs/articles/appendix/08_differential_abundance_analysis_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/09_latent_Dirichlet_allocation.html
docs/articles/appendix/09_latent_Dirichlet_allocation_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/10_uncertainity_quan_ordination.html
docs/articles/appendix/10_uncertainity_quan_ordination_files/header-attrs-2.9/header-attrs.js
docs/articles/appendix/BNO_all.png
docs/articles/appendix/Rhat_plant_all_K_11.png
docs/articles/appendix/circular_plot_plant_all_K_11.png
docs/articles/appendix/ess_bulk_plant_all_K_11.png
docs/articles/appendix/goodness_of_fit_nb_taxa.png
docs/articles/appendix/model_assesment_hist_all_obs_sim_K_11.png
docs/articles/appendix/topic_dis_all_11.png
docs/articles/diffTop.html
docs/articles/diffTop_files/header-attrs-2.9/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/LDAtopicmodel.html
docs/reference/Rplot001.png
docs/reference/alignmentMatrix.html
docs/reference/betaAligned.html
docs/reference/dds_all_K_11.html
docs/reference/dds_all_paired_K_11.html
docs/reference/dds_all_paired_aster_K_11.html
docs/reference/dds_all_paired_nonaster_K_11.html
docs/reference/diagnosticsPlot.html
docs/reference/diffTop-package.html
docs/reference/diffTopAnalysis.html
docs/reference/index.html
docs/reference/modelAssessment.html
docs/reference/phyloseqTransformation.html
docs/reference/plotASVCircular.html
docs/reference/plotTopicProportion.html
docs/reference/powerstand.html
docs/reference/powerswitch.html
docs/reference/psE.html
docs/reference/psE_BARBI.html
docs/reference/ps_ans.html
docs/reference/setUpData.html
docs/reference/thetaAligned.html
docs/reference/writeResTable.html
inst/include/stan_meta_header.hpp
inst/stan/include/license.stan
inst/stan/lda.stan
man/LDAtopicmodel.Rd man/alignmentMatrix.Rd man/betaAligned.Rd man/dds_all_K_11.Rd man/dds_all_paired_K_11.Rd man/dds_all_paired_aster_K_11.Rd man/dds_all_paired_nonaster_K_11.Rd man/diagnosticsPlot.Rd man/diffTop-package.Rd man/diffTopAnalysis.Rd man/modelAssessment.Rd man/phyloseqTransformation.Rd man/plotASVCircular.Rd man/plotTopicProportion.Rd man/powerstand.Rd man/powerswitch.Rd man/psE.Rd man/psE_BARBI.Rd man/ps_ans.Rd man/setUpData.Rd man/thetaAligned.Rd man/writeResTable.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/stanExports_lda.cc
src/stanExports_lda.h
vignettes/.gitignore
vignettes/appendix/01_introduction.Rmd vignettes/appendix/02_microbiome_data.Rmd vignettes/appendix/03_example_16S_data.Rmd vignettes/appendix/04_models.Rmd vignettes/appendix/05_transformation.Rmd vignettes/appendix/06_visualization.Rmd vignettes/appendix/07_multivariate_and_network_analysis.Rmd vignettes/appendix/08_differential_abundance_analysis.Rmd vignettes/appendix/09_latent_Dirichlet_allocation.Rmd vignettes/appendix/10_uncertainity_quan_ordination.Rmd
vignettes/appendix/BNO_all.png
vignettes/appendix/Rhat_plant_all_K_11.png
vignettes/appendix/circular_plot_plant_all_K_11.png
vignettes/appendix/ess_bulk_plant_all_K_11.png
vignettes/appendix/goodness_of_fit_nb_taxa.png
vignettes/appendix/model_assesment_hist_all_obs_sim_K_11.png
vignettes/appendix/topic_dis_all_11.png
vignettes/diffTop.Rmd
vignettes/library.bib
PratheepaJ/diffTop documentation built on Dec. 18, 2021, 7:48 a.m.

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