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VCA (version 1.3.2)

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 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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Version

Install

install.packages('VCA')

Monthly Downloads

1,651

Version

1.3.2

License

GPL (>= 3)

Maintainer

Andre Schuetzenmeister

Last Published

July 25th, 2016

Functions in VCA (1.3.2)

as.matrix.VCA

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

Build a Nested List.
chol2invData

Dataset Generating Error in Function 'chol2inv'
as.matrix.VCAinference

Standard 'as.matrix' Method for 'VCAinference' S3-Objects.
check4MKL

Check for Availability of Intel's Math Kernel Library.
coef.VCA

Extract Fixed Effects from 'VCA' Object.
anovaDF

ANOVA Type-I Degrees of Freedom.
anovaMM

ANOVA-Type Estimation of Mixed Models.
anovaVCA

ANOVA-Type Estimation of Variance Components for Random Models.
CA19_9

Reproducibility Example Dataset from CLSI EP05-A3
dataRS0003_1

Simulated Repeated Measurements Data.
dataEP05A2_2

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
dataEP05A3_MS_2

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site 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_3

Simulated Data of a CLSI EP05-A3 3/5/5 Multi-Site Experiment
dataRS0003_2

Simulated Repeated Measurements Data.
Csweep

Calling C-implementation of the SWEEP-Operator
dataRS0003_3

Simulated Repeated Measurements Data.
dataEP05A2_1

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

Determine A-Matrix.
dataRS0005_1

Simulated Data of 5/3 Experiment.
getDF

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

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

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

Extract Fixed Effects from 'VCA' Object.
fixef

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

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

ANOVA Sum of Squares via Quadratic Forms
HugeData

Huge Dataset with Three Variables
Glucose

Inermediate Precision Data from CLSI EP05-A3
getMat

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

Covariance-Matrix of Variance Components.
getL

Construct Linear Contrast Matrix for Hypothesis Tests.
getGB

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

Overparameterized Design Matrices.
getSSQsweep

ANOVA Sum of Squares via Sweeping.
lmerMatrices

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

Load 'RevoUtilsMath'-package if available.
lmerSummary

MPinv

Moore-Penrose Generalized Inverse of a Matrix.
isBalanced

Check Whether Design Is Balanced Or Not.
plot.VCA

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

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

Orthodont dataset from R-package 'nlme'
lsmeans

Least Squares Means of Fixed Effects.
lsmMat

Contrast Matrix for LS Means.
remlMM

Fit Linear Mixed Models via REML.
print.VCAinference

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

Real-World Data
ranef.VCA

Extract Random Effects from 'VCA' Object.
ranef

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

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

Variability Chart for Hierarchical Models.
Trace

Compute the Trace of a Matrix.
residuals.VCA

Extract Residuals of a 'VCA' Object.
ReproData1

Multi-Site Data for Estimating Reproducibility Precision
VCAinference

Inferential Statistics for VCA-Results.
test.fixef

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

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

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

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

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

Calculate Variance-Covariance Matrix of Variance Components of 'VCA' objects.
test.lsmeans

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

Solve Mixed Model Equations.
stepwiseVCA

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

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

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

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

sleepstudy dataset from R-package 'lme4'
VCA-package

(V)ariance (C)omponent (A)nalysis.
VCAdata1

Simulated Data for Variance Component Analysis.