mirix: Calculate Microbiome Response Index (MiRIx) values

In tuv292/abx_idx: Modeling the Susceptibility of a Bacterial Community to Antibiotics

Calculate Microbiome Response Index (MiRIx) values

Description

Calculate Microbiome Response Index (MiRIx) values

Usage

mirix(abundance, susceptibility, replace_zero = 1e-04)

Arguments

abundance	A vector of taxon abundances in a sample
susceptibility	A character vector of taxon susceptibility, with values that are "susceptible", "resistant", or NA
replace_zero	Zero-replacement value. If the numerator or denominator is smaller than this value, they will be replaced with the number here. This number should generally be slightly less than the minimum measurement that could be acquired with the method used. For count data, a value of 0.5 is typical. For relative abundances, a number that is slightly lower than the lowest relative abundance will work.

Value

The MiRIx value

tuv292/abx_idx documentation built on Jan. 12, 2023, 12:48 a.m.