calc_residuals: Calculate residuals for Correspondence analysis

In VingronLab/APL: Association Plots

Calculate residuals for Correspondence analysis

Description

calc_residuals provides optional residuals as the basis for Correspondence Analysis

Usage

calc_residuals(mat, residuals = "pearson", clip = FALSE, cutoff = NULL)

Arguments

mat	A numerical matrix or coercible to one by 'as.matrix()'. Should have row and column names.
residuals	character string. Specifies which kind of residuals should be calculated. Can be "pearson" (default), "freemantukey" or "NB" for negative-binomial.
clip	logical. Whether residuals should be clipped if they are higher/lower than a specified cutoff
cutoff	numeric. Residuals that are larger than cutoff or lower than -cutoff are clipped to cutoff.

Value

A named list. The elements are:

• "S": standardized residual matrix.

• "tot": grand total of the original matrix.

• "rowm": row masses.

• "colm": column masses.

VingronLab/APL documentation built on Nov. 9, 2024, 5:33 p.m.