throat.tree: UPGMA tree of the OTUs from 16S sequencing of the throat...

In MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests

Description

The OTU tree is constructed using UPGMA on the K80 distance matrice of the OTUs. It is a rooted tree of class "phylo".

Usage

data(throat.tree)

Format

The format is: chr "throat.tree"

Details

The OTUs are produced by the QIIME software. Singleton OTUs have been discarded.

Source

Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, et al. (2010) Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers. PLoS ONE 5(12): e15216.

Examples

data(throat.tree)
## maybe str(throat.tree) ; plot(throat.tree) ...

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: ape
Loading required package: aSPU
Loading required package: gee
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

The following objects are masked from ‘package:base’:

    backsolve, forwardsolve

See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: matrixStats
Loading required package: cluster

MiSPU documentation built on May 1, 2019, 8:41 p.m.