integralSystem: Make Lotka-Volterra coefficient system

In AlmaasLab/micInt: Find microbial interactions

Make Lotka-Volterra coefficient system

Description

This function accepts time series of OTU measurements and the linear equation system for its coefficients, as described in cited article.

Usage

integralSystem(time_series, kind = "integral", removeZeros = TRUE)

Arguments

time_series	An OTU_time_series or a list of them If a list is passed, the OTUs must be the same and in the same order in each of the sub-objects.
kind	Charachter, one of c('integral','log_integral') Choose whether use the integral or log-integral approach described in the article cited.
removeZeros	Logical, for the 'integral' option, remove the equations which produce zero rows. This is ignored for the 'log_integral' because in that case, all two consecutive measurements which contains a zero for the OTU in question, must be discared anyway.

Value

A list of lists (one for each OTU) with two elements:

• A The coefficient matrix for the system

• b The right side of the system

References

P. H. Kloppers and J. C. Greeff. “Lotka-Volterra model parameter estimation using experiential data”. In: Appl. Math. Comput. 224 (Nov. 2013), pp. 817–825. ISSN: 0096-3003. DOI: https://doi.org/10.1016/j.amc.2013.08.093

Examples

library(micInt)
library(phyloseq)
data("seawater")
subsetted_seawater <- subset_samples(seawater, Reactor == 2)
integralSystem(OTU_time_series(subsetted_seawater,"Week"), kind = "log_integral")

AlmaasLab/micInt documentation built on April 1, 2022, 10:37 a.m.