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VCA (version 1.4.5)

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

843

Version

1.4.5

License

GPL (>= 3)

Maintainer

Andre Schuetzenmeister

Last Published

September 7th, 2022

Functions in VCA (1.4.5)

anovaMM

ANOVA-Type Estimation of Mixed Models
Trace

Compute the Trace of a Matrix
anovaVCA

ANOVA-Type Estimation of Variance Components for Random Models
VCA-package

(V)ariance (C)omponent (A)nalysis.
as.matrix.VCA

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

Standard 'as.matrix' Method for 'VCAinference' S3-Objects
VCAdata1

Simulated Data for Variance Component Analysis.
Scale

Automatically Scale Data Calling these Functions: 'anovaVCA', 'anovaMM', 'remlVCA' or 'remlMM'
VCAinference

Inferential Statistics for VCA-Results
Solve

Solve System of Linear Equations using Inverse of Cholesky-Root
chol2invData

Dataset Generating Error in Function 'chol2inv'
buildList

Build a Nested List.
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_1

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
check4MKL

Check for Availability of Intel's Math Kernel Library
dataEP05A2_3

Simulated Data of a CLSI EP05-A2 20/2/2 Experiment
dataRS0005_1

Simulated Data of 5/3 Experiment.
dataRS0003_1

Simulated Repeated Measurements Data.
dataRS0003_3

Simulated Repeated Measurements Data.
dataRS0003_2

Simulated Repeated Measurements Data.
dataRS0005_3

Simulated Data of 5/3 Experiment.
getMM

Overparameterized Design Matrices
getV

Determine V-Matrix for a 'VCA' Object
isBalanced

Check Whether Design Is Balanced Or Not
getL

Construct Linear Contrast Matrix for Hypothesis Tests
dataRS0005_2

Simulated Data of 5/3 Experiment.
getDF

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

Extract a Specific Matrix from a 'VCA' Object
getDDFM

Degrees of Freedom for Testing Linear Contrasts of Fixed Effects and Least Square Means
coef.VCA

Extract Fixed Effects from 'VCA' Object
getSSQsweep

ANOVA Sum of Squares via Sweeping
lmerMatrices

Derive and Compute Matrices for Objects Fitted by Function 'lmer'
lmerSummary

Derive VCA-Summary Table from an Object Fitted via Function lmer
lsmMat

Contrast Matrix for LS Means
load_if_installed

Load 'RevoUtilsMath'-package if available
getGB

Giesbrecht & Burns Approximation of the Variance-Covariance Matrix of Variance Components
dataEP05A3_MS_3

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

Extract Fixed Effects from 'VCA' Object
fixef

Generic Method for Extracting Fixed Effects from a Fitted Model
model.matrix.VCA

Model Matrix of a Fitted VCA-Object
orderData

Re-Order Data.Frame
fitVCA

Fit Variance Component Model by ANOVA or REML
dataEP05A3_MS_1

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

Fit Linear Mixed Model by ANOVA or REML
legend.m

Add Legend to Margin.
model.frame.VCA

Extract the Model Frame from a 'VCA' Object
lsmeans

Least Squares Means of Fixed Effects
realData

Real-World Data
getIP.remlVCA

Intermediate Precision for remlVCA-fitted objects of class 'VCA'
remlMM

Fit Linear Mixed Models via REML
ranef.VCA

Extract Random Effects from 'VCA' Object
reScale

Re-Scale results of 'VCA' or 'VCAinference'
predict.VCA

Predictions from a Model Fitted by fitLMM
print.VCA

Standard Printing Method for Objects of Class 'VCA'
plotRandVar

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

Standard 'plot' Method for 'VCA' S3-Objects.
print.VCAinference

Standard Print Method for Objects of Class 'VCAinference'
lmerG

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

Generic Method for Extracting Random Effects from a Fitted Model
scaleData

Scale Response Variable to Ensure Robust Numerical Calculations
test.lsmeans

Perform t-Tests for Linear Contrasts on LS Means
remlVCA

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

Perform t-Tests for Linear Contrasts on Fixed Effects
residuals.VCA

Extract Residuals of a 'VCA' Object
solveMME

Solve Mixed Model Equations
sleepstudy

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

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

Variability Chart for Hierarchical Models.
stepwiseVCA

Bottom-Up Step-Wise VCA-Analysis of the Complete Dataset
ReproData1

Multi-Site Data for Estimating Reproducibility Precision
Fsweep

Calling F90-implementation of the SWEEP-Operator
MPinv

Moore-Penrose Generalized Inverse of a Matrix
SattDF

Satterthwaite Approximation for Total Degrees of Freedom and for Single Variance Components
DfSattHelper

Variance-Covariance Matrix of Fixed Effects as Function of Covariance Parameter Estimates
Glucose

Inermediate Precision Data from CLSI EP05-A3
MLrepro

Multi-Lot Reproducibility Data.
HugeData

Huge Dataset with Three Variables
Orthodont

Orthodont dataset from R-package 'nlme'
CA19_9

Reproducibility Example Dataset from CLSI EP05-A3