R: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

# North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

## Documentation for package ‘OTUtable’ version 1.1.2

- DESCRIPTION file

## Help Pages

OTUtable-package | OTU table analysis functions
bog_subset | Subset OTU table by sampling site
chao1 | Chao1 Richness
clean_mothur_taxonomy | Clean mothur-format Taxonomy File
clean_shared | Reformat a shared file
clean_TaxAss_taxonomy | Clean Taxonomy File Output by TaxAss Workflow
combine_otus | Combine OTUs based on identical taxonomic assignments
extract_date | Extract sampling date from a vector of sample names
filter_taxa | Filter Taxa Based on Abundance and Persistence
grab_group | Subset OTU table by taxonomic assignment
make_do_matrix | Make matrix of dissolved oxygen data
make_temp_matrix | Make matrix of temperature data
metadata | Lake metadata for OTU table
obs_richness | Observed Richness
OTUtable | OTU table analysis functions
otu_table | OTU table generated from 8 bog lakes over 4 years
pielou | Pielou's Evenness
plot_column | Plot DO or temperature data from a depth profile over time
reduce_names | Shorten taxonomic assignment in table row names
remove_reps | Remove the second replicate of each sample, when it exists
rotate | Rotate a matrix
shannon | Shannon's Biodiversity Index
taxonomy | Taxonomic assignments of OTUs
year_subset | Subset samples by a specific year
zscore | Z-score normalize relative abundance data