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OTUtable (version 1.1.2)

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

Description

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," .

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Version

Install

install.packages('OTUtable')

Monthly Downloads

160

Version

1.1.2

License

GPL-3

Maintainer

Alexandra Linz

Last Published

May 26th, 2018

Functions in OTUtable (1.1.2)

taxonomy

Taxonomic assignments of OTUs
year_subset

Subset samples by a specific year
zscore

Z-score normalize relative abundance data
pielou

Pielou's Evenness
shannon

Shannon's Biodiversity Index
filter_taxa

Filter Taxa Based on Abundance and Persistence
combine_otus

Combine OTUs based on identical taxonomic assignments
clean_shared

Reformat a shared file
clean_TaxAss_taxonomy

Clean Taxonomy File Output by TaxAss Workflow
OTUtable-package

OTU table analysis functions
extract_date

Extract sampling date from a vector of sample names
chao1

Chao1 Richness
bog_subset

Subset OTU table by sampling site
obs_richness

Observed Richness
plot_column

Plot DO or temperature data from a depth profile over time
metadata

Lake metadata for OTU table
reduce_names

Shorten taxonomic assignment in table row names
clean_mothur_taxonomy

Clean mothur-format Taxonomy File
grab_group

Subset OTU table by taxonomic assignment
remove_reps

Remove the second replicate of each sample, when it exists
rotate

Rotate a matrix
make_do_matrix

Make matrix of dissolved oxygen data
make_temp_matrix

Make matrix of temperature data
otu_table

OTU table generated from 8 bog lakes over 4 years