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

Documentation for package ‘OTUtable’ version 1.1.2

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