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

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. (2016) "Seasonal mixing as a barrier to the development of stable bacterial communities in bog lakes" (Manuscript in prep).

Author
Alexandra Linz
Date of publication
2016-03-17 18:59:27
Maintainer
Alexandra Linz <amlinz16@gmail.com>
License
GPL-3
Version
1.0.0

View on CRAN

Man pages

bog_subset
Subset OTU table by sampling site
chao1
Chao1 Richness
clean_shared
Reformat a shared file
clean_taxonomy
Clean Taxonomy File
combine_otus
Combine OTUs based on identical taxonomic assignments
extract_date
Extract sampling date from a vector of sample names
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

Files in this package

OTUtable
OTUtable/NAMESPACE
OTUtable/data
OTUtable/data/otu_table.rda
OTUtable/data/metadata.rda
OTUtable/data/taxonomy.rda
OTUtable/R
OTUtable/R/format_mothur_output.R
OTUtable/R/data_processing.R
OTUtable/R/water_column_plots.R
OTUtable/R/OTUtable.R
OTUtable/R/alpha_biodiversity_metrics.R
OTUtable/MD5
OTUtable/DESCRIPTION
OTUtable/man
OTUtable/man/make_do_matrix.Rd
OTUtable/man/bog_subset.Rd
OTUtable/man/grab_group.Rd
OTUtable/man/otu_table.Rd
OTUtable/man/metadata.Rd
OTUtable/man/shannon.Rd
OTUtable/man/zscore.Rd
OTUtable/man/rotate.Rd
OTUtable/man/plot_column.Rd
OTUtable/man/reduce_names.Rd
OTUtable/man/taxonomy.Rd
OTUtable/man/combine_otus.Rd
OTUtable/man/clean_shared.Rd
OTUtable/man/extract_date.Rd
OTUtable/man/clean_taxonomy.Rd
OTUtable/man/OTUtable-package.Rd
OTUtable/man/chao1.Rd
OTUtable/man/obs_richness.Rd
OTUtable/man/pielou.Rd
OTUtable/man/make_temp_matrix.Rd
OTUtable/man/year_subset.Rd
OTUtable/man/remove_reps.Rd