R: Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres

# Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres

## Documentation for package ‘otuSummary’ version 0.1.2

- DESCRIPTION file
- Package README

## Help Pages

alphaDiversity | Calculate the alpha diversity indices
bplot | Generate barplot with custom controls on the x axis labels
calc_bc | calculate the Bray-Curtis dissimilarity
contrib | Contribution of rare/abundant biosphere to the total Bray-Curtis dissimilarity
fillTax | reshape the heirarchical taxonomy
fillTax2 | reshape the heirarchical taxonomy
matrixConvert | Convert lower triangular distance matrix into data frame
otu4type | An example OTU table with samples and taxonomy in rows and otus in columns
otuCollap | collapse a OTU table at given level.
otumothur | OTU table generated from 8 lakes over 4 years
otuqiime | OTU table generated from 8 lakes over 4 years
otuReport | Summarize the community structure and abundance with OTU table
pbray | Partition the Bray-Curtis distance dissimilarity
rareBiosphere | Summarize different subgroups in the rare biosphere
slimTax | reshape heirarchical taxonomy
subOTU | Subset a OTU table
typeConvert | Transpose the data frame if there is data type conversion.