VCA: Variance Component Analysis
Version 1.3.2

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.

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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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("VCA")

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

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

Files

inst
inst/UnitTests
inst/UnitTests/runit.VCAinference.R
inst/UnitTests/SASresultsRealData_Model1_by_PID_Lot.txt
inst/UnitTests/runit.misc.R
inst/UnitTests/runit.remlVCA.R
inst/UnitTests/runit.anovaVCA.R
inst/UnitTests/runit.remlMM.R
inst/UnitTests/runit.anovaMM.R
inst/UnitTests/RunAllTests.R
inst/UnitTests/SASresultsRealData_Model2_by_PID.txt
inst/ChangeLog.txt
src
src/vca.c
NAMESPACE
data
data/dataEP05A2_3.RData
data/dataRS0005_1.RData
data/dataEP05A3_MS_2.RData
data/dataRS0005_2.RData
data/sleepstudy.RData
data/dataEP05A3_MS_1.RData
data/dataRS0003_3.RData
data/dataRS0003_1.RData
data/chol2invData.RData
data/CA19_9.RData
data/dataRS0003_2.RData
data/realData.RData
data/HugeData.RData
data/dataEP05A2_1.RData
data/dataRS0005_3.RData
data/dataEP05A3_MS_3.RData
data/VCAdata1.RData
data/Orthodont.RData
data/ReproData1.RData
data/dataEP05A2_2.RData
data/Glucose.RData
R
R/vca.R
R/plot.R
MD5
DESCRIPTION
man
man/getGB.Rd
man/as.matrix.VCAinference.Rd
man/dataRS0003_1.Rd
man/anovaVCA.Rd
man/chol2invData.Rd
man/SattDF.Rd
man/dataEP05A2_3.Rd
man/Sinv.Rd
man/dataRS0005_1.Rd
man/vcov.VCA.Rd
man/DfSattHelper.Rd
man/getSSQqf.Rd
man/dataEP05A2_1.Rd
man/lsmeans.Rd
man/ReproData1.Rd
man/varPlot.Rd
man/dataRS0003_2.Rd
man/Csweep.Rd
man/ranef.Rd
man/Trace.Rd
man/Glucose.Rd
man/print.VCAinference.Rd
man/VCA-Package.Rd
man/realData.Rd
man/test.lsmeans.Rd
man/lmerG.Rd
man/sleepstudy.Rd
man/dataEP05A2_2.Rd
man/getDF.Rd
man/vcovVC.Rd
man/dataRS0005_3.Rd
man/remlMM.Rd
man/getSSQsweep.Rd
man/remlVCA.Rd
man/stepwiseVCA.Rd
man/VCAdata1.Rd
man/getMat.Rd
man/lsmMat.Rd
man/check4MKL.Rd
man/plot.VCA.Rd
man/buildList.Rd
man/dataEP05A3_MS_3.Rd
man/print.VCA.Rd
man/getDDFM.Rd
man/dataRS0003_3.Rd
man/getVCvar.Rd
man/solveMME.Rd
man/getAmatrix.Rd
man/vcovFixed.Rd
man/dataEP05A3_MS_2.Rd
man/anovaMM.Rd
man/lmerMatrices.Rd
man/getL.Rd
man/residuals.VCA.Rd
man/MPinv.Rd
man/isBalanced.Rd
man/anovaDF.Rd
man/VCAinference.Rd
man/fixef.Rd
man/test.fixef.Rd
man/lmerSummary.Rd
man/coef.VCA.Rd
man/dataEP05A3_MS_1.Rd
man/dataRS0005_2.Rd
man/as.matrix.VCA.Rd
man/plotRandVar.Rd
man/HugeData.Rd
man/getMM.Rd
man/load_if_installed.Rd
man/getCmatrix.Rd
man/ranef.VCA.Rd
man/Orthodont.Rd
man/Solve.Rd
man/fixef.VCA.Rd
man/CA19_9.Rd
man/getV.Rd
VCA documentation built on May 19, 2017, 10:19 p.m.