simulate.MM: shell script for creating the simulation

In Djeppschmidt/Model.Microbiome: Environment And Community Simulation Package

shell script for creating the simulation

Description

shell script for creating the simulation

Usage

## S3 method for class 'MM'
simulate(reps, commonN, groupN, singleN, D, V, method, Spike = T, Interact = T)

Arguments

reps	number of replicate communities
commonN	number of common species
groupN	number of unique taxa to groups
singleN	number of unique taxa to samples
D	average sampling depth
V	variation in sampling depth
method	list of function names to be used in analysis
Spike	whether or not to use the spike in functions. If spike==T, then any normalization function that does not include using the spike in, should filter the spikein before doing other normalization steps.
interact	whether or not have taxa interact

Examples

test.script<-benchmark.MM(reps=3, commonN=20, groupN=10, singleN=10, D=2000, V=1000)
benchmark.MM()

Djeppschmidt/Model.Microbiome documentation built on Sept. 17, 2022, 9:15 p.m.