# Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

## Documentation for package ‘themetagenomics’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cnn | Normalize an OTU table by 16S rRNA copy number
DAVID | Human longitudinal microbiome data
download_ref | Download functional prediction reference tables
est | Estimate topic or function effects
est.functions | Estimate predicted function-topic effects
est.hmc | Estimate predicted function-topic effects
est.ml | Estimate predicted function-topic effects
est.topics | Estimate topic effects
est_functions | Estimate predicted function-topic effects
est_topics | Estimate topic effects
extract | Extract summary statistics
extract.effects | Extract summary statistics
find_topics | Perform topic estimation on a themetadata object
GEVERS | Inflammatory bowel disease gut microbiome data
picrust | Predict OTU functional content via PICRUSt
picrust_otu | Predict OTU functional potential via PICRUSt
predict.functions | Predict topic functional content
predict.topics | Predict topic functional content
predict_functions | Predict topic functional content
predict_topics | Predict topic functional content
prepare_data | Prepare themetadata object from data for topic modeling pipeline
resume | Resume HMC using a previous fit
resume.effects | Resume HMC using a previous fit
s | Make a B-spline Basis Function (from 's')
t4f | Predict taxonomic functional content via tax4fun
vis | Launch in interactive visualize to explore topic effects
vis.binary | Launch in interactive visualize to explore topic effects
vis.continuous | Launch in interactive visualize to explore topic effects
vis.effects | Launch in interactive visualize to explore topic effects
vis.functions | Launch in interactive visualize to explore topic effects
vis.taxa | Launch in interactive visualize to explore topic effects
vis.topics | Launch in interactive visualize to explore topic effects