VCA: Variance Component Analysis

ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.

AuthorAndre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Date of publication2016-07-25 20:30:17
MaintainerAndre Schuetzenmeister <andre.schuetzenmeister@roche.com>
LicenseGPL (>= 3)
Version1.3.2

View on CRAN

Man pages

anovaDF: ANOVA Type-I Degrees of Freedom.

anovaMM: ANOVA-Type Estimation of Mixed Models.

anovaVCA: ANOVA-Type Estimation of Variance Components for Random...

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

as.matrix.VCAinference: Standard 'as.matrix' Method for 'VCAinference' S3-Objects.

buildList: Build a Nested List.

CA19_9: Reproducibility Example Dataset from CLSI EP05-A3

check4MKL: Check for Availability of Intel's Math Kernel Library.

chol2invData: Dataset Generating Error in Function 'chol2inv'

coef.VCA: Extract Fixed Effects from 'VCA' Object.

Csweep: Calling C-implementation of the SWEEP-Operator

dataEP05A2_1: Simulated Data of a CLSI EP05-A2 20/2/2 Experiment

dataEP05A2_2: Simulated Data of a CLSI EP05-A2 20/2/2 Experiment

dataEP05A2_3: Simulated Data of a CLSI EP05-A2 20/2/2 Experiment

dataEP05A3_MS_1: Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment

dataEP05A3_MS_2: Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment

dataEP05A3_MS_3: Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment

dataRS0003_1: Simulated Repeated Measurements Data.

dataRS0003_2: Simulated Repeated Measurements Data.

dataRS0003_3: Simulated Repeated Measurements Data.

dataRS0005_1: Simulated Data of 5/3 Experiment.

dataRS0005_2: Simulated Data of 5/3 Experiment.

dataRS0005_3: Simulated Data of 5/3 Experiment.

DfSattHelper: Variance-Covariance Matrix of Fixed Effects as Function of...

fixef: Generic Method for Extracting Fixed Effects from a Fitted...

fixef.VCA: Extract Fixed Effects from 'VCA' Object.

getAmatrix: Determine A-Matrix.

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

getDDFM: Degrees of Freedom for Testing Linear Contrast of Fixed...

getDF: Extract Degrees of Freedom from Linear Hypotheses of Fixed...

getGB: Giesbrecht & Burns Approximation of the Variance-Covariance...

getL: Construct Linear Contrast Matrix for Hypothesis Tests.

getMat: Extract a Specific Matrix from a 'VCA' Object.

getMM: Overparameterized Design Matrices.

getSSQqf: ANOVA Sum of Squares via Quadratic Forms

getSSQsweep: ANOVA Sum of Squares via Sweeping.

getV: Determine V-Matrix for a 'VCA' Object.

getVCvar: Covariance-Matrix of Variance Components.

Glucose: Inermediate Precision Data from CLSI EP05-A3

HugeData: Huge Dataset with Three Variables

isBalanced: Check Whether Design Is Balanced Or Not.

lmerG: Construct Variance-Covariance Matrix of Random Effects for...

lmerMatrices: Derive and Compute Matrices for Objects Fitted by Function...

lmerSummary: Derive VCA-Summary Table from an Object Fitted via Function...

load_if_installed: Load 'RevoUtilsMath'-package if available.

lsmeans: Least Squares Means of Fixed Effects.

lsmMat: Contrast Matrix for LS Means.

MPinv: Moore-Penrose Generalized Inverse of a Matrix.

Orthodont: Orthodont dataset from R-package 'nlme'

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

plot.VCA: Standard 'plot' Method for 'VCA' S3-Objects.

print.VCA: Standard Printing Method for Objects of Class 'VCA'.

print.VCAinference: Standard Print Method for Objects of Class 'VCAinference'.

ranef: Generic Method for Extracting Random Effects from a Fitted...

ranef.VCA: Extract Random Effects from 'VCA' Object.

realData: Real-World Data

remlMM: Fit Linear Mixed Models via REML.

remlVCA: Perform (V)ariance (C)omponent (A)nalysis via...

ReproData1: Multi-Site Data for Estimating Reproducibility Precision

residuals.VCA: Extract Residuals of a 'VCA' Object.

SattDF: Satterthwaite Approximation for Total Degrees of Freedom and...

Sinv: Calling C-implementation of the SWEEP-Operator for...

sleepstudy: sleepstudy dataset from R-package 'lme4'

Solve: Solve System of Linear Equations using Inverse of...

solveMME: Solve Mixed Model Equations.

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

test.fixef: Perform t-Tests for Linear Contrasts on Fixed Effects.

test.lsmeans: Perform t-Tests for Linear Contrasts on LS Means.

Trace: Compute the Trace of a Matrix.

varPlot: Variability Chart for Hierarchical Models.

VCAdata1: Simulated Data for Variance Component Analysis.

VCAinference: Inferential Statistics for VCA-Results.

VCA-Package: (V)ariance (C)omponent (A)nalysis.

vcovFixed: Calculate Variance-Covariance Matrix and Standard Errors of...

vcovVC: Calculate Variance-Covariance Matrix of Variance Components...

vcov.VCA: Calculate Variance-Covariance Matrix of Fixed Effects for an...

Functions

anovaDF Man page
anovaMM Man page
anovaVCA Man page
as.matrix.VCA Man page
as.matrix.VCAinference Man page
buildList Man page
CA19_9 Man page
check4MKL Man page
chol2invData Man page
coef.VCA Man page
Csweep Man page
dataEP05A2_1 Man page
dataEP05A2_2 Man page
dataEP05A2_3 Man page
dataEP05A3_MS_1 Man page
dataEP05A3_MS_2 Man page
dataEP05A3_MS_3 Man page
dataRS0003_1 Man page
dataRS0003_2 Man page
dataRS0003_3 Man page
dataRS0005_1 Man page
dataRS0005_2 Man page
dataRS0005_3 Man page
DfSattHelper Man page
fixef Man page
fixef.VCA Man page
getAmatrix Man page
getCmatrix Man page
getDDFM Man page
getDF Man page
getGB Man page
getL Man page
getMat Man page
getMM Man page
getSSQqf Man page
getSSQsweep Man page
getV Man page
getVCvar Man page
Glucose Man page
HugeData Man page
isBalanced Man page
lmerG Man page
lmerMatrices Man page
lmerSummary Man page
load_if_installed Man page
lsmeans Man page
lsmMat Man page
MPinv Man page
Orthodont Man page
plotRandVar Man page
plot.VCA Man page
print.VCA Man page
print.VCAinference Man page
ranef Man page
ranef.VCA Man page
realData Man page
remlMM Man page
remlVCA Man page
ReproData1 Man page
resid Man page
residuals.VCA Man page
SattDF Man page
Sinv Man page
sleepstudy Man page
Solve Man page
solveMME Man page
stepwiseVCA Man page
test.fixef Man page
test.lsmeans Man page
Trace Man page
varPlot Man page
VCA Man page
VCAdata1 Man page
VCAinference Man page
VCA-package Man page
vcovFixed Man page
vcovVC Man page
vcov.VCA Man page

Files

VCA
VCA/inst
VCA/inst/UnitTests
VCA/inst/UnitTests/runit.VCAinference.R
VCA/inst/UnitTests/SASresultsRealData_Model1_by_PID_Lot.txt
VCA/inst/UnitTests/runit.misc.R
VCA/inst/UnitTests/runit.remlVCA.R
VCA/inst/UnitTests/runit.anovaVCA.R
VCA/inst/UnitTests/runit.remlMM.R
VCA/inst/UnitTests/runit.anovaMM.R
VCA/inst/UnitTests/RunAllTests.R
VCA/inst/UnitTests/SASresultsRealData_Model2_by_PID.txt
VCA/inst/ChangeLog.txt
VCA/src
VCA/src/vca.c
VCA/NAMESPACE
VCA/data
VCA/data/dataEP05A2_3.RData
VCA/data/dataRS0005_1.RData
VCA/data/dataEP05A3_MS_2.RData
VCA/data/dataRS0005_2.RData
VCA/data/sleepstudy.RData
VCA/data/dataEP05A3_MS_1.RData
VCA/data/dataRS0003_3.RData
VCA/data/dataRS0003_1.RData
VCA/data/chol2invData.RData
VCA/data/CA19_9.RData
VCA/data/dataRS0003_2.RData
VCA/data/realData.RData
VCA/data/HugeData.RData
VCA/data/dataEP05A2_1.RData
VCA/data/dataRS0005_3.RData
VCA/data/dataEP05A3_MS_3.RData
VCA/data/VCAdata1.RData
VCA/data/Orthodont.RData
VCA/data/ReproData1.RData
VCA/data/dataEP05A2_2.RData
VCA/data/Glucose.RData
VCA/R
VCA/R/vca.R VCA/R/plot.R
VCA/MD5
VCA/DESCRIPTION
VCA/man
VCA/man/getGB.Rd VCA/man/as.matrix.VCAinference.Rd VCA/man/dataRS0003_1.Rd VCA/man/anovaVCA.Rd VCA/man/chol2invData.Rd VCA/man/SattDF.Rd VCA/man/dataEP05A2_3.Rd VCA/man/Sinv.Rd VCA/man/dataRS0005_1.Rd VCA/man/vcov.VCA.Rd VCA/man/DfSattHelper.Rd VCA/man/getSSQqf.Rd VCA/man/dataEP05A2_1.Rd VCA/man/lsmeans.Rd VCA/man/ReproData1.Rd VCA/man/varPlot.Rd VCA/man/dataRS0003_2.Rd VCA/man/Csweep.Rd VCA/man/ranef.Rd VCA/man/Trace.Rd VCA/man/Glucose.Rd VCA/man/print.VCAinference.Rd VCA/man/VCA-Package.Rd VCA/man/realData.Rd VCA/man/test.lsmeans.Rd VCA/man/lmerG.Rd VCA/man/sleepstudy.Rd VCA/man/dataEP05A2_2.Rd VCA/man/getDF.Rd VCA/man/vcovVC.Rd VCA/man/dataRS0005_3.Rd VCA/man/remlMM.Rd VCA/man/getSSQsweep.Rd VCA/man/remlVCA.Rd VCA/man/stepwiseVCA.Rd VCA/man/VCAdata1.Rd VCA/man/getMat.Rd VCA/man/lsmMat.Rd VCA/man/check4MKL.Rd VCA/man/plot.VCA.Rd VCA/man/buildList.Rd VCA/man/dataEP05A3_MS_3.Rd VCA/man/print.VCA.Rd VCA/man/getDDFM.Rd VCA/man/dataRS0003_3.Rd VCA/man/getVCvar.Rd VCA/man/solveMME.Rd VCA/man/getAmatrix.Rd VCA/man/vcovFixed.Rd VCA/man/dataEP05A3_MS_2.Rd VCA/man/anovaMM.Rd VCA/man/lmerMatrices.Rd VCA/man/getL.Rd VCA/man/residuals.VCA.Rd VCA/man/MPinv.Rd VCA/man/isBalanced.Rd VCA/man/anovaDF.Rd VCA/man/VCAinference.Rd VCA/man/fixef.Rd VCA/man/test.fixef.Rd VCA/man/lmerSummary.Rd VCA/man/coef.VCA.Rd VCA/man/dataEP05A3_MS_1.Rd VCA/man/dataRS0005_2.Rd VCA/man/as.matrix.VCA.Rd VCA/man/plotRandVar.Rd VCA/man/HugeData.Rd VCA/man/getMM.Rd VCA/man/load_if_installed.Rd VCA/man/getCmatrix.Rd VCA/man/ranef.VCA.Rd VCA/man/Orthodont.Rd VCA/man/Solve.Rd VCA/man/fixef.VCA.Rd VCA/man/CA19_9.Rd VCA/man/getV.Rd

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