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VCA (version 1.1.1)

Variance Component Analysis

Description

ANOVA-type estimation (prediction) of random effects and variance components in linear mixed models, is implemented. Random models, a sub-set of mixed models, can be fit applying a Variance Component Analysis (VCA). This is a special type of analysis frequently used in verifying the precision performance of diagnostics. The Satterthwaite approximation of the total degrees of freedom is implemented. There are several functions for extracting, random effects, fixed effects, variance-covariance matrices of random and fixed effects. Residuals can be extracted as raw, standardized and studentized residuals. Additionally, a variability chart is implemented for visualizing the variability in sub-classes emerging from an experimental design ('varPlot').

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Version

Install

install.packages('VCA')

Monthly Downloads

1,476

Version

1.1.1

License

GPL (>= 3)

Maintainer

Andre Schuetzenmeister

Last Published

April 27th, 2015

Functions in VCA (1.1.1)

VCAdata1

Simulated Data for Variance Component Analysis.
dataEP05A2_2

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
VCAinference

Inferential Statistics for VCA-Results.
dataRS0003_3

Simulated Repeated Measurements Data.
Trace

Compute the Trace of a Matrix.
getMM

Overparameterized Design Matrices.
SattDF

Satterthwaite Approximation for Total Degrees of Freedom and for Single Variance Components.
fixef

Generic Method for Extracting Fixed Effects from a Fitted Model.
coef.VCA

Extract Fixed Effects from 'VCA' Object.
DfSattHelper

Variance-Covariance Matrix of Fixed Effects as Function of Covariance Parameter Estimates.
dataRS0003_2

Simulated Repeated Measurements Data.
dataRS0005_3

Simulated Data of 5/3 Experiment.
dataEP05A2_1

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
anovaMM

ANOVA-Type Estimation of Mixed Models.
test.fixef

Perform t-Tests for Linear Contrasts on Fixed Effects.
realData

Real-World Data
buildList

Build a Nested List.
Orthodont

Orthodont dataset from R-package 'nlme'
dataEP05A2_3

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
as.matrix.VCA

Standard 'as.matrix' Method for 'VCA' S3-Objects.
dataEP05A2_example

Example Data from CLSI EP05-A2
print.VCAinference

Standard Print Method for Objects of Class 'VCAinference'.
ranef.VCA

Extract Random Effects from 'VCA' Object.
isBalanced

Check Whether Design Is Balanced Or Not.
anovaDF

ANOVA Type-I Degrees of Freedom.
dataEP05A3_MS_2

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment
plotRandVar

Plot Random Variates of a Mixed Model ('VCA' Object).
getDDFM

Degrees of Freedom for Testing Linear Contrast of Fixed Effects and Least Square Means.
getCmatrix

Coefficient Matrix for (V)ariance (C)omponent (A)nalysis.
MPinv

Moore-Penrose Inverse of a Matrix.
lsmeans

Least Squares Means of Fixed Effects.
getMat

Extract a Specific Matrix from a 'VCA' Object.
getL

Construct Linear Contrast Matrix for Hypothesis Tests.
getDF

Extract Degrees of Freedom from Linear Hypotheses of Fixed Effects or LS Means.
fixef.VCA

Extract Fixed Effects from 'VCA' Object.
test.lsmeans

Perform t-Tests for Linear Contrasts on LS Means.
dataRS0005_1

Simulated Data of 5/3 Experiment.
getV

Determine V-Matrix for a 'VCA' Object.
dataRS0003_1

Simulated Repeated Measurements Data.
ranef

Generic Method for Extracting Random Effects from a Fitted Model.
dataRS0005_2

Simulated Data of 5/3 Experiment.
stepwiseVCA

Bottom-Up Step-Wise VCA-Analysis of the Complete Dataset.
print.VCA

Standard Printing Method for Objects of Class 'VCA'.
solveMM

Solve Mixed Model Equations.
anovaVCA

ANOVA-Type Estimation of Variance Components for Random Models.
vcovFixed

Calculate Variance-Covariance Matrix and Standard Errors of Fixed Effects for an 'VCA' Object.
lsmMat

Contrast Matrix for LS Means.
residuals.VCA

Extract Residuals of a 'VCA' Object.
dataEP05A3_MS_1

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment
getAmatrix

Determine A-Matrix.
vcov.VCA

Calculate Variance-Covariance Matrix of Fixed Effects for an 'VCA' Object.
vcovVC

Calculate Variance-Covariance Matrix of Variance Components of 'VCA' objects.
dataEP05A3_MS_3

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment
varPlot

Variability Chart for Hierarchical Models.
VCA-package

(V)ariance (C)omponent (A)nalysis.
getVCvar

Covariance-Matrix of Variance Components.