Calculate s-dimensional rotated random effects

Description

This function calculates reduced dimensional rotated random effects. The rotation reduces the influence of the residuals from other levels of the model so that distributional assessment of the resulting random effects is possible.

Usage

## Default S3 method:
rotate_ranef(.mod, ...)

## S3 method for class 'mer'
rotate_ranef(.mod, .L, s = NULL, .varimax = FALSE, ...)

## S3 method for class 'lmerMod'
rotate_ranef(.mod, .L, s = NULL, .varimax = FALSE, ...)

## S3 method for class 'lme'
rotate_ranef(.mod, .L, s = NULL, .varimax = FALSE, ...)

Arguments

Author(s)

Adam Loy loyad01@gmail.com

References

Loy, A. & Hofmann, H. (in press). Are you Normal? The Problem of Confounded Residual Structures in Hierarchical Linear Models. Journal of Computational and Graphical Statistics.

Examples

library(lme4)
fm <- lmer(log.radon ~ basement + uranium + (basement | county), data = radon)

ngrps <- summary(fm)$ngrps
L.b0  <- kronecker(Diagonal(ngrps), c(1, 0))
L.b1  <- kronecker(Diagonal(ngrps), c(0, 1))

b0.rot <- rotate_ranef(.mod = fm, .L = L.b0, s = 65, .varimax = TRUE)
qqnorm(b0.rot)

b1.rot <- rotate_ranef(.mod = fm, .L = L.b1, s = 65, .varimax = TRUE)
qqnorm(b1.rot)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HLMdiag)

Attaching package: 'HLMdiag'

The following object is masked from 'package:stats':

    covratio

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HLMdiag/rotate_ranef.mer.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rotate_ranef.default
> ### Title: Calculate s-dimensional rotated random effects
> ### Aliases: rotate_ranef rotate_ranef.default rotate_ranef.lme
> ###   rotate_ranef.lmerMod rotate_ranef.mer
> 
> ### ** Examples
> 
> library(lme4)
Loading required package: Matrix
> fm <- lmer(log.radon ~ basement + uranium + (basement | county), data = radon)
> 
> ngrps <- summary(fm)$ngrps
> L.b0  <- kronecker(Diagonal(ngrps), c(1, 0))
> L.b1  <- kronecker(Diagonal(ngrps), c(0, 1))
> 
> b0.rot <- rotate_ranef(.mod = fm, .L = L.b0, s = 65, .varimax = TRUE)
Note: method with signature 'diagonalMatrix#Matrix' chosen for function 'kronecker',
 target signature 'ddiMatrix#dgCMatrix'.
 "ANY#sparseMatrix" would also be valid
Note: method with signature 'dsparseMatrix#dsparseMatrix' chosen for function 'kronecker',
 target signature 'dtTMatrix#dgCMatrix'.
 "TsparseMatrix#sparseMatrix" would also be valid
> qqnorm(b0.rot)
> 
> b1.rot <- rotate_ranef(.mod = fm, .L = L.b1, s = 65, .varimax = TRUE)
> qqnorm(b1.rot)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>