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VCA (version 1.3.4)

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

1,041

Version

1.3.4

License

GPL (>= 3)

Maintainer

Andre Schuetzenmeister

Last Published

July 18th, 2018

Functions in VCA (1.3.4)

Compute the Trace of a Matrix.

Generic Method for Extracting Fixed Effects from a Fitted Model.

Simulated Data of 5/3 Experiment.

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

Build a Nested List.

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

ANOVA Sum of Squares via Sweeping.

Inermediate Precision Data from CLSI EP05-A3

Extract Fixed Effects from 'VCA' Object.

Get Orthogonal Basis of a Matrix.

ANOVA-Type Estimation of Mixed Models.

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

Dataset Generating Error in Function 'chol2inv'

dataEP05A3_MS_2

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

Simulated Repeated Measurements Data.

Generic Method for Extracting Random Effects from a Fitted Model.

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

Huge Dataset with Three Variables

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

Automatically Scale Data Calling These Functions: 'anovaVCA', 'anovaMM', 'remlVCA' or 'remlMM'.

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

model.matrix.VCA

Model Matrix of a Fitted VCA-Object.

Fit Linear Mixed Model by ANOVA or REML.

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

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

Covariance-Matrix of Variance Components.

Simulated Data for Variance Component Analysis.

Scale Response Variable to Ensure Robust Numerical Calculations.

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

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

Re-Order Data.Frame.

load_if_installed

Load 'RevoUtilsMath'-package if available.

Multi-Site Data for Estimating Reproducibility Precision

Check for Availability of Intel's Math Kernel Library.

Perform t-Tests for Linear Contrasts on LS Means.

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

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

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

ANOVA Sum of Squares via Quadratic Forms

print.VCAinference

Standard Print Method for Objects of Class 'VCAinference'.

Fit Variance Component Model by ANOVA or REML.

Perform t-Tests for Linear Contrasts on Fixed Effects.

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

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

Determine A-Matrix.

Multi-Lot Reproducibility Data.

Add Legend to Margin.

model.frame.VCA

Extract the Model Frame from a 'VCA' Object.

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

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

Contrast Matrix for LS Means.

Simulated Data of 5/3 Experiment.

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

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

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

Simulated Data of 5/3 Experiment.

Determine V-Matrix for a 'VCA' Object.

Solve Mixed Model Equations.

Extract Fixed Effects from 'VCA' Object.

Reproducibility Example Dataset from CLSI EP05-A3

ANOVA Type-I Degrees of Freedom.

dataEP05A3_MS_1

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

Inferential Statistics for VCA-Results.

Extract Random Effects from 'VCA' Object.

Check Whether Design Is Balanced Or Not.

Re-Scale results of 'VCA' or 'VCAinference' objects which were constructed using scaled values of the response variable.

Moore-Penrose Generalized Inverse of a Matrix.

Fit Linear Mixed Models via REML.

Standard Printing Method for Objects of Class 'VCA'.

Orthodont dataset from R-package 'nlme'

Predictions from a Model Fitted by fitLMM.

Real-World Data

Least Squares Means of Fixed Effects.

Extract a Specific Matrix from a 'VCA' Object.

Calling C-implementation of the SWEEP-Operator

Construct Linear Contrast Matrix for Hypothesis Tests.

as.matrix.VCAinference

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

sleepstudy dataset from R-package 'lme4'

Simulated Repeated Measurements Data.

Simulated Repeated Measurements Data.

Overparameterized Design Matrices.

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

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

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

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

Extract Residuals of a 'VCA' Object.

Variability Chart for Hierarchical Models.