RAM (version 1.2.0)

assist.NB: Negative Binomial Test For OTUID or Taxon

Description

This function does negative binomial test for a given otuID or taxon

Usage

assist.NB(data, meta, is.OTU=TRUE, rank=NULL, meta.factors=NULL,
          anov.fac=NULL, taxon="")

Arguments

data

an ecology data set to be analyzed.

meta

the metadata table to be analyzed.

is.OTU

logical. If an OTU table was provided, is.OTU should be set as TRUE; otherwise, it should be set as FALSE.

rank

optional. If no rank was provided, the data will be used as it is, if rank is provided, if data is an OTU table, it will be converted to taxonomic abundance matrix at the given rank, no change will be made for a data that has al

meta.factors

optional. If provided, will only test the model on selected metadata variables; otherwise, will test all variables in the metadata table.

anov.fac

optional. Whether or not to do anova test on a metadata variable.

taxon

a length one charactor. Can either be an otuID or a taxon name.

Value

• This function return a list of outputs of the negative bionomial modeling for a selected otuID or taxa. Members of this output list are: "NB.model", "tax.met", "taxon", "factors", "anova".
• NB.model
  is the negative bionomial model
• tax.met
  is a dataframe with combined the taxon and metadata
• taxon
  is either a taxon name or in LCA_otuID format, see also LCA.OTU
• factors
  shows which metadata variable had significant impact
• anova
  shows anova test of a metadata variable, this will not be available if anov.fac is NULL

Examples

data(ITS1, meta)
m <- meta[, c(2,3,5,7)]
# for usage demonstration purpose only, may not fit the negative 
# binomial distribution model.
nb <- assist.NB(ITS1, meta=m, rank="g", anov.fac="Harvestmethod", 
              taxon=rownames(ITS1)[1])