North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions
Subset OTU table by sampling site
Chao1 Richness
Clean mothur-format Taxonomy File
Reformat a shared file
Clean Taxonomy File Output by TaxAss Workflow
Combine OTUs based on identical taxonomic assignments
Extract sampling date from a vector of sample names
Filter Taxa Based on Abundance and Persistence
Subset OTU table by taxonomic assignment
Make matrix of dissolved oxygen data
Make matrix of temperature data
Observed Richness
OTU table analysis functions
Pielou's Evenness
Plot DO or temperature data from a depth profile over time
Shorten taxonomic assignment in table row names
Remove the second replicate of each sample, when it exists
Rotate a matrix
Shannon's Biodiversity Index
Subset samples by a specific year
Z-score normalize relative abundance data
Analyses of OTU tables produced by 16S rRNA gene amplicon sequencing, as well as example data. It contains the data and scripts used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes," <doi: 10.1128/mSphere.00169-17>.