# HMP-package: Hypothesis Testing and Power Calculations for Comparing... In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

## Description

This package provides tools for Generating data matrices following Multinomial and Dirichlet-Multinomial distributions, Computing the following test-statistics and their corresponding p-values, and Computing the power and size of the tests described above using Monte-Carlo simulations.

## Details

 \textbf{Hypothesis Test} \textbf{Test Statistics Function} \textbf{Power Calculation Function} 2+ Sample Means w/ Reference Vector `Xmc.sevsample` `MC.Xmc.statistics` 1 Sample Mean w/ Reference Vector `Xsc.onesample` `MC.Xsc.statistics` 2+ Sample Means w/o Reference Vector `Xmcupo.sevsample` `MC.Xmcupo.statistics` 2+ Sample Overdispersions `Xoc.sevsample` `MC.Xoc.statistics` 2+ Sample DM-Distribution `Xdc.sevsample` `MC.Xdc.statistics` Multinomial vs DM `C.alpha.multinomial` `MC.ZT.statistics`

In addition to hypothesis testing and power calculations you can:

1. Perform basic data management to exclude samples with fewer than pre-specified number of reads, collapse rare taxa and order the taxa by frequency. This is useful to exclude failed samples (i.e. samples with very few reads) - `Data.filter`

2. Plot your data - `Barchart.data`

3. Generate random sample of Dirichlet Multinomial data with pre-specified parameters - `Dirichlet.multinomial`

Note: Thought the description of the functions refer its application to ranked abundance distributions (RAD) data, every function is also applicable to model species abundance data. See references for a discussion and application to both type of ecological data.

## Author(s)

Patricio S. La Rosa, Elena Deych, Berkley Shands, Sharina Carter, Dake Yang, William D. Shannon

## References

La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, et al. (2012) Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data. PLoS ONE 7(12): e52078. doi:10.1371/journal.pone.0052078

Yang D, Johnson J, Zhou X, Deych E, et al. (2019) Microbiome Recursive Partitioning. Currently Under Review.

HMP documentation built on Aug. 31, 2019, 5:05 p.m.