This is a repository with my commonly-shared scripts for familiarizing new students with R and microbial ecology analyses.
1. read_data_and_metadata_readxl
This contains an R script and example data. The objective is to read in datasheet with both sample metadata + data to R using the readxl package, then split into two dataframes (data and metadata).
2. quick_ASV_analyses
This contains an R script and example data. The objective is to read in a processed amplicon datasheet (with both data and metadata) to R using the readxl package, and to conduct various quick analyses (NMDS ordination, taxonomy barplots, diversity calculations) using the vegan and ggplot2 packages.
3. procrustes_envfit
This contains an R script and example data. The objective is to read in two datasets (metabolite and amplicon) to R, generate two ordinations, calculate significant loadings, and run a procrustes analysis between the two ordinations.