limits: LIMITS

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

LIMITS

Description

LIMITS is an algorithm developed by Fisher & Mehta to estimate the interaction matrix from time series data assuming a Ricker model.

Usage

limits(x, indices.perturb = NA, bagging.iter = 100, verbose = FALSE)

Arguments

x	time series with taxa as rows and time points as columns
indices.perturb	indices of species considered as environmental parameters
bagging.iter	the number of iterations used for bagging
verbose	print which taxon LIMITS is processing

Value

a list with the estimated interaction matrix as Aest and the estimation error as error

References

Fisher & Mehta (2014). Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries using Sparse Linear Regression. PLoS One 9:e102451

Examples

## Not run: 
N=20
A=generateA(N,c=0.1)
ts=ricker(N=N,A=A)
Aest=limits(ts,verbose=TRUE)$Aest
par(mfrow=c(2,1))
plotA(A,header="original")
plotA(Aest,header="estimated")
par(mfrow=c(1,1))

## End(Not run)

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.