assist.NB: Negative Binomial Test For OTUID or Taxon
In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description Usage Arguments Value Author(s) Examples

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

1 2	assist.NB(data, meta, is.OTU=TRUE, rank=NULL, meta.factors=NULL, anov.fac=NULL, taxon="")

`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 already been a taxonomic abundance matrix. See also `tax.abund` and `data.revamp`
`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.

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`

Wen Chen

data(ITS1, meta)
m <- meta[, c(2,3,5,7)]
## Not run: 
# 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])

## End(Not run)