# Variance Component Analysis

## Documentation for package ‘VCA’ version 1.5.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

VCA-package | (V)ariance (C)omponent (A)nalysis.
anovaMM | ANOVA-Type Estimation of Mixed Models
anovaVCA | ANOVA-Type Estimation of Variance Components for Random Models
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
checkData | Check Random Model for Given Dataset.
checkVars | Check Tow Formula Terms for Potential Problems.
chol2invData | Dataset Generating Error in Function 'chol2inv'
coef.VCA | Extract Fixed Effects from 'VCA' Object
combineVC | Combine Variance Components and Adjust Degrees of Freedom.
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 Covariance Parameter Estimates
errorMessage | Convert Objects to Detailed Error Message.
fitLMM | Fit Linear Mixed Model by ANOVA or REML
fitVCA | Fit Variance Component Model by ANOVA or REML
fixef | Generic Method for Extracting Fixed Effects from a Fitted Model
fixef.VCA | Extract Fixed Effects from 'VCA' Object
Fsweep | Calling F90-implementation of the SWEEP-Operator
getCI | Extract Confidence Intervals from VCA-Objects.
getDDFM | Degrees of Freedom for Testing Linear Contrasts of Fixed Effects and Least Square Means
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
getIP.remlVCA | Intermediate Precision for remlVCA-fitted objects of class 'VCA'
getL | Construct Linear Contrast Matrix for Hypothesis Tests
getMat | Extract a Specific Matrix from a 'VCA' Object
getMM | Overparameterized Design Matrices
getSSQsweep | ANOVA Sum of Squares via Sweeping
getV | Determine V-Matrix for a 'VCA' Object
Glucose | Inermediate Precision Data from CLSI EP05-A3
HugeData | Huge Dataset with Three Variables
isBalanced | Check Whether Design Is Balanced Or Not
legend.m | Add Legend to Margin.
lmerG | Construct Variance-Covariance Matrix of Random Effects for Models Fitted by Function 'lmer'
lmerMatrices | Derive and Compute Matrices for Objects Fitted by Function 'lmer'
lmerSummary | Derive VCA-Summary Table from an Object Fitted via Function 'lmer'
load_if_installed | Load 'RevoUtilsMath'-package if available
lsmeans | Least Squares Means of Fixed Effects
LSMeans_Data | Dataset for Unit-Testing of LS Means
lsmMat | Contrast Matrix for LS Means
MLrepro | Multi-Lot Reproducibility Data.
model.frame.VCA | Extract the Model Frame from a 'VCA' Object
model.matrix.VCA | Model Matrix of a Fitted VCA-Object
MPinv | Moore-Penrose Generalized Inverse of a Matrix
orderData | Re-Order Data.Frame
Orthodont | Orthodont dataset from R-package 'nlme'
plot.VCA | Standard 'plot' Method for 'VCA' S3-Objects.
plotRandVar | Plot Random Variates of a Mixed Model ('VCA' Object).
predict.VCA | Predictions from a Model Fitted by 'fitLMM'
print.VCA | Standard Printing Method for Objects of Class 'VCA'
print.VCAinference | Standard Print Method for Objects of Class 'VCAinference'
protectedCall | Wrap Function-Calls to Execute Additional Checks.
ranef | Generic Method for Extracting Random Effects from a Fitted Model
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 REML-Estimation
ReproData1 | Multi-Site Data for Estimating Reproducibility Precision
reScale | Re-Scale results of 'VCA' or 'VCAinference'
resid | Extract Residuals of a 'VCA' Object
residuals.VCA | Extract Residuals of a 'VCA' Object
SattDF | Satterthwaite Approximation for Total Degrees of Freedom and for Single Variance Components
Scale | Automatically Scale Data Calling these Functions: 'anovaVCA', 'anovaMM', 'remlVCA' or 'remlMM'
scaleData | Scale Response Variable to Ensure Robust Numerical Calculations
sleepstudy | sleepstudy dataset from R-package 'lme4'
Solve | Solve System of Linear Equations using Inverse of Cholesky-Root
solveMME | Solve Mixed Model Equations
stepwiseVCA | Bottom-Up Step-Wise VCA-Analysis of the Complete Dataset
summarize.VCA | Summarize Outcome of a Variance Component Analysis.
summarize.VCAinference | Summarize Outcome of a Variance Component Analysis.
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.
VCA | (V)ariance (C)omponent (A)nalysis.
VCAdata1 | Simulated Data for Variance Component Analysis.
VCAinference | Inferential Statistics for VCA-Results
vcov.VCA | Calculate Variance-Covariance Matrix of Fixed Effects for an 'VCA' Object
vcovFixed | Calculate Variance-Covariance Matrix and Standard Errors of Fixed Effects for an 'VCA' Object
vcovVC | Calculate Variance-Covariance Matrix of Variance Components of 'VCA' objects