Variance Component Analysis

Documentation for package ‘VCA’ version 1.5.1

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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
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