VCA: Variance Component Analysis

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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.

Author
Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Date of publication
2016-07-25 20:30:17
Maintainer
Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
License
GPL (>= 3)
Version
1.3.2

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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...

Files in this package

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