get_r2-mat: Function for unexplained variance ratio calculation indicated...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Function for unexplained variance ratio calculation indicated in Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32–46.

Usage

## S4 method for signature 'matrix,ANY,ANY'
get_r2(x, des, group)

## S4 method for signature 'matrix,data.frame,ANY'
get_r2(x, des, group)

## S4 method for signature 'matrix,data.frame,character'
get_r2(x, des, group = c("Host_genotype", "Compartment", "Soil", "Management"))

Arguments

x	Dissimilarity / distance matrix which indicate variances.
des	The descriptive table of samples which define the groups.
group	The name(s) of column(s) used as experimental setup group(s) in descriptive file.

Value

r2 The variance ratio cannot be explained by given groups.

Examples

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref")
maize <- fit_tabs(maize)
maize <- com_dis(maize, method = "bray")
x <- dis(maize)
des <- des(maize)
get_r2(x, des, group = c("Compartment", "Soil"))

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.