OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions
Version 1.1.0

Analyses of OTU tables produced by 16S 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" (Manuscript submitted, preprint available at ).

AuthorAlexandra Linz
Date of publication2017-04-13 18:01:29 UTC
MaintainerAlexandra Linz <amlinz16@gmail.com>
LicenseGPL-3
Version1.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("OTUtable")

Getting started

Package overview

Popular man pages

bog_subset: Subset OTU table by sampling site
clean_mothur_taxonomy: Clean mothur-format Taxonomy File
combine_otus: Combine OTUs based on identical taxonomic assignments
obs_richness: Observed Richness
OTUtable-package: OTU table analysis functions
rotate: Rotate a matrix
zscore: Z-score normalize relative abundance data
See all...

All man pages Function index File listing

Man pages

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_otus: 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
otu_table: OTU table generated from 8 bog lakes over 4 years
OTUtable-package: OTU table analysis functions
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

Functions

OTUtable Man page
OTUtable-package Man page
bog_subset Man page Source code
chao1 Man page Source code
clean_TaxAss_taxonomy Man page Source code
clean_mothur_taxonomy Man page Source code
clean_shared Man page Source code
combine_otus Man page Source code
extract_date Man page Source code
filter_taxa Man page Source code
grab_group Man page Source code
make_do_matrix Man page Source code
make_temp_matrix Man page Source code
metadata Man page
obs_richness Man page Source code
otu_table Man page
pielou Man page Source code
plot_column Man page Source code
reduce_names Man page Source code
remove_reps Man page Source code
rotate Man page Source code
shannon Man page Source code
taxonomy Man page
year_subset Man page Source code
zscore Man page Source code

Files

NAMESPACE
data
data/otu_table.rda
data/metadata.rda
data/taxonomy.rda
R
R/format_mothur_output.R
R/data_processing.R
R/water_column_plots.R
R/OTUtable.R
R/alpha_biodiversity_metrics.R
MD5
DESCRIPTION
man
man/make_do_matrix.Rd
man/bog_subset.Rd
man/grab_group.Rd
man/otu_table.Rd
man/metadata.Rd
man/shannon.Rd
man/zscore.Rd
man/rotate.Rd
man/plot_column.Rd
man/reduce_names.Rd
man/taxonomy.Rd
man/combine_otus.Rd
man/clean_shared.Rd
man/extract_date.Rd
man/clean_mothur_taxonomy.Rd
man/filter_otus.Rd
man/OTUtable-package.Rd
man/chao1.Rd
man/obs_richness.Rd
man/pielou.Rd
man/make_temp_matrix.Rd
man/year_subset.Rd
man/remove_reps.Rd
man/clean_TaxAss_taxonomy.Rd
OTUtable documentation built on May 19, 2017, 8:28 a.m.

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