excercises.Rmd

---
title: "Radboud Course 2022: Practicals"
author: "Anna Aatsinki"
date: '2022-07-04'
output: html_document
---

## Exercises

### Alpha diversity

- Calculate alpha diversity indices

- Test if data agglomeration to higher taxonomic ranks affects the indices

- Look for differences in alpha diversity between groups or correlation with a continuous variable


### Beta diversity

- Visualize community variation with different methods (PCA, MDS, NMDS, etc.) with plotReduceDim and with different dissimilarities and transformations,plot also other than the first two axes.

- Use PERMANOVA to test differences in beta diversity. You can also try including continuous and/or categorical covariates

- If there are statistical differences in PERMANOVA, test PERMDISP2 (betadisper function)

- Do DMM clustering

- Try RDA to test the variance explained by external variables


Seek guidance from the [https://microbiome.github.io/OMA/](https://microbiome.github.io/OMA/)