clr: CLR transformation of community matrix, with multiplicative...

In Russel88/MicEco: Various functions for microbial community data

CLR transformation of community matrix, with multiplicative zero replacement

Description

This function performs a CLR transformation on the input. Prior to transformation it does a multiplicative zero replacement, which adds a pseudocount, but corrects the non-zero abundances such that log-ratios between non-zero elements are unchanged after correction.

Usage

clr(mat, delta = 1)

Arguments

mat	A community matrix with features as rows
delta	The pseudocount to exchange zeroes with. Zero-correction is multiplicative such that the log-ratios between any entirely non-zero features will not be affected by the pseudocount.

Value

CLR transformed community matrix

Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.