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VCA (version 1.3.1)

Variance Component Analysis

Description

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 a perform 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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Version

Install

install.packages('VCA')

Monthly Downloads

1,476

Version

1.3.1

License

GPL (>= 3)

Maintainer

Andre Schuetzenmeister

Last Published

April 4th, 2016

Functions in VCA (1.3.1)

Orthodont

Orthodont dataset from R-package 'nlme'
CA19_9

Reproducibility Example Dataset from CLSI EP05-A3
Sinv

Calling C-implementation of the SWEEP-Operator for Matrix-Inversion
DfSattHelper

Variance-Covariance Matrix of Fixed Effects as Function of Covariance Parameter Estimates.
chol2invData

Dataset Generating Error in Function 'chol2inv'
fixef.VCA

Extract Fixed Effects from 'VCA' Object.
VCAdata1

Simulated Data for Variance Component Analysis.
dataRS0005_3

Simulated Data of 5/3 Experiment.
getMat

Extract a Specific Matrix from a 'VCA' Object.
VCA-package

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

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

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

Giesbrecht & Burns Approximation of the Variance-Covariance Matrix of Variance Components.
anovaMM

ANOVA-Type Estimation of Mixed Models.
lmerG

Construct Variance-Covariance Matrix of Random Effects for Models Fitted by Function 'lmer'.
getDDFM

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

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

ANOVA Sum of Squares via Quadratic Forms
solveMME

Solve Mixed Model Equations.
Csweep

Calling C-implementation of the SWEEP-Operator
lsmeans

Least Squares Means of Fixed Effects.
residuals.VCA

Extract Residuals of a 'VCA' Object.
lmerMatrices

Derive and Compute Matrices for Objects Fitted by Function 'lmer'.
HugeData

Huge Dataset with Three Variables
Solve

Solve System of Linear Equations using Inverse of Cholesky-Root.
anovaDF

ANOVA Type-I Degrees of Freedom.
Trace

Compute the Trace of a Matrix.
getL

Construct Linear Contrast Matrix for Hypothesis Tests.
dataRS0005_2

Simulated Data of 5/3 Experiment.
fixef

Generic Method for Extracting Fixed Effects from a Fitted Model.
lmerSummary

Derive VCA-Summary Table from an object fitted via function lmer.
getMM

Overparameterized Design Matrices.
dataRS0003_2

Simulated Repeated Measurements Data.
realData

Real-World Data
stepwiseVCA

Bottom-Up Step-Wise VCA-Analysis of the Complete Dataset.
dataEP05A3_MS_1

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

Determine A-Matrix.
getV

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

Inferential Statistics for VCA-Results.
plotRandVar

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

Build a Nested List.
dataEP05A2_3

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

sleepstudy dataset from R-package 'lme4'
dataRS0003_1

Simulated Repeated Measurements Data.
vcov.VCA

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

Covariance-Matrix of Variance Components.
SattDF

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

Moore-Penrose Inverse of a Matrix.
print.VCA

Standard Printing Method for Objects of Class 'VCA'.
ReproData1

Multi-Site Data for Estimating Reproducibility Precision
ranef.VCA

Extract Random Effects from 'VCA' Object.
getCmatrix

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

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

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

Variability Chart for Hierarchical Models.
dataEP05A2_1

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
dataRS0003_3

Simulated Repeated Measurements Data.
remlMM

Fit Linear Mixed Models via REML.
dataRS0005_1

Simulated Data of 5/3 Experiment.
getSSQsweep

ANOVA Sum of Squares via Sweeping.
print.VCAinference

Standard Print Method for Objects of Class 'VCAinference'.
dataEP05A3_MS_2

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment
coef.VCA

Extract Fixed Effects from 'VCA' Object.
remlVCA

Perform (V)ariance (C)omponent (A)nalysis via REML-Estimation.
vcovFixed

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

Standard 'as.matrix' Method for 'VCA' S3-Objects.
dataEP05A2_2

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

Inermediate Precision Data from CLSI EP05-A3
anovaVCA

ANOVA-Type Estimation of Variance Components for Random Models.
dataEP05A3_MS_3

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

Contrast Matrix for LS Means.
load_if_installed

Load 'RevoUtilsMath'-package if available.
isBalanced

Check Whether Design Is Balanced Or Not.
check4MKL

Check for Availability of Intel's Math Kernel Library.