# Tools for Model Specification in the Latent Variable Framework

## Documentation for package ‘lavaSearch2’ version 1.5.6

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

## Help Pages

A C D E F G I L M N R S T V misc

lavaSearch2-package | Tools for Model Specification in the Latent Variable Framework

## -- A --

addLink | Add a New Link Between Two Variables in a LVM
addLink.lvm | Add a New Link Between Two Variables in a LVM
addLink.lvm.reduced | Add a New Link Between Two Variables in a LVM
autoplot.calibrateType1 | Graphical Display of the Bias or Type 1 Error
autoplot.intDensTri | 2D-display of the Domain Used to Compute the Integral
autoplot.modelsearch2 | Display the Value of a Coefficient across the Steps.
autoplot_calibrateType1 | Graphical Display of the Bias or Type 1 Error
autplot-modelsearch2 | Display the Value of a Coefficient across the Steps.

## -- C --

calcDistMax | Adjust the p.values Using the Quantiles of the Max Statistic
calcDistMaxBootstrap | Adjust the p.values Using the Quantiles of the Max Statistic
calcDistMaxIntegral | Adjust the p.values Using the Quantiles of the Max Statistic
calcType1postSelection | Compute the Type 1 Error After Selection [EXPERIMENTAL]
calibrateType1 | Simulation Study Assessing Bias and Type 1 Error
calibrateType1.lvm | Simulation Study Assessing Bias and Type 1 Error
calibrateType1.lvmfit | Simulation Study Assessing Bias and Type 1 Error
checkData | Check that Validity of the Dataset
checkData.lvm | Check that Validity of the Dataset
clean | Simplify a lvm object
clean.lvm | Simplify a lvm object
coefByType | Extract the Coefficient by Type
coefCov | Extract the Coefficient by Type
coefCov.lvm | Extract the Coefficient by Type
coefCov.lvmfit | Extract the Coefficient by Type
coefCov.multigroup | Extract the Coefficient by Type
coefExtra | Extract the Coefficient by Type
coefExtra.lvm | Extract the Coefficient by Type
coefExtra.lvmfit | Extract the Coefficient by Type
coefExtra.multigroup | Extract the Coefficient by Type
coefIndexModel | Extract the Coefficient by Type
coefIndexModel.lvm | Extract the Coefficient by Type
coefIndexModel.lvmfit | Extract the Coefficient by Type
coefIndexModel.multigroup | Extract the Coefficient by Type
coefIndexModel.multigroupfit | Extract the Coefficient by Type
coefIntercept | Extract the Coefficient by Type
coefIntercept.lvm | Extract the Coefficient by Type
coefIntercept.lvmfit | Extract the Coefficient by Type
coefIntercept.multigroup | Extract the Coefficient by Type
coefRef | Extract the Coefficient by Type
coefRef.lvmfit | Extract the Coefficient by Type
coefReg | Extract the Coefficient by Type
coefReg.lvm | Extract the Coefficient by Type
coefReg.lvmfit | Extract the Coefficient by Type
coefReg.multigroup | Extract the Coefficient by Type
coefType | Extract the Type of Each Coefficient
coefType.lvm | Extract the Type of Each Coefficient
coefType.lvmfit | Extract the Type of Each Coefficient
coefType.multigroup | Extract the Type of Each Coefficient
coefVar | Extract the Coefficient by Type
coefVar.lvm | Extract the Coefficient by Type
coefVar.lvmfit | Extract the Coefficient by Type
coefVar.multigroup | Extract the Coefficient by Type
combineFormula | Combine formula
compare2 | Test Linear Hypotheses with small sample correction
compare2.gls | Test Linear Hypotheses with small sample correction
compare2.gls2 | Test Linear Hypotheses with small sample correction
compare2.lm | Test Linear Hypotheses with small sample correction
compare2.lm2 | Test Linear Hypotheses with small sample correction
compare2.lme | Test Linear Hypotheses with small sample correction
compare2.lme2 | Test Linear Hypotheses with small sample correction
compare2.lvmfit | Test Linear Hypotheses with small sample correction
compare2.lvmfit2 | Test Linear Hypotheses with small sample correction
convFormulaCharacter | formula character conversion
createContrast | Create Contrast matrix
createContrast.character | Create Contrast matrix
createContrast.gls | Create Contrast matrix
createContrast.list | Create Contrast matrix
createContrast.lm | Create Contrast matrix
createContrast.lme | Create Contrast matrix
createContrast.lvmfit | Create Contrast matrix
createContrast.mmm | Create Contrast matrix

## -- D --

dfSigma | Degree of Freedom for the Chi-Square Test
dfSigmaRobust | Degree of Freedom for the Robust Chi-Square Test

## -- E --

effects2 | Effects from a fitted model
effects2.lvmfit | Effects from a fitted model
effects2.lvmfit2 | Effects from a fitted model
estfun | Extract Empirical Estimating Functions (lvmfit Object)
estfun.gls | Extract Empirical Estimating Functions (lvmfit Object)
estfun.lme | Extract Empirical Estimating Functions (lvmfit Object)
estfun.lvmfit | Extract Empirical Estimating Functions (lvmfit Object)
extractData | Extract Data From a Model
extractData.coxph | Extract Data From a Model
extractData.cph | Extract Data From a Model
extractData.gls | Extract Data From a Model
extractData.lm | Extract Data From a Model
extractData.lme | Extract Data From a Model
extractData.lvmfit | Extract Data From a Model

## -- F --

findNewLink | Find all New Links Between Variables
findNewLink.lvm | Find all New Links Between Variables
formula2character | formula character conversion

## -- G --

getNewLink | Extract the Links that Have Been Found by the modelsearch2.
getNewLink.modelsearch2 | Extract the Links that Have Been Found by the modelsearch2.
getNewModel | Extract the Model that Has Been Retains by the modelsearch2.
getNewModel.modelsearch2 | Extract the Model that Has Been Retains by the modelsearch2.
getStep | Extract one Step From the Sequential Procedure
getStep.modelsearch2 | Extract one Step From the Sequential Procedure
getVarCov2 | Reconstruct the Conditional Variance Covariance Matrix
getVarCov2.gls | Reconstruct the Conditional Variance Covariance Matrix
getVarCov2.lme | Reconstruct the Conditional Variance Covariance Matrix
getVarCov2.lvmfit | Reconstruct the Conditional Variance Covariance Matrix
glht2 | General Linear Hypothesis
glht2.lvmfit | General Linear Hypothesis
glht2.mmm | General Linear Hypothesis

## -- I --

iid2 | Extract corrected i.i.d. decomposition
iid2.gls | Extract corrected i.i.d. decomposition
iid2.gls2 | Extract corrected i.i.d. decomposition
iid2.lm | Extract corrected i.i.d. decomposition
iid2.lm2 | Extract corrected i.i.d. decomposition
iid2.lme | Extract corrected i.i.d. decomposition
iid2.lme2 | Extract corrected i.i.d. decomposition
iid2.lvmfit | Extract corrected i.i.d. decomposition
iid2.lvmfit2 | Extract corrected i.i.d. decomposition
iidJack | Jackknife iid Decomposition from Model Object
iidJack.default | Jackknife iid Decomposition from Model Object
information2 | Extract The full Information Matrix
information2.gls | Extract The full Information Matrix
information2.gls2 | Extract The full Information Matrix
information2.lm | Extract The full Information Matrix
information2.lm2 | Extract The full Information Matrix
information2.lme | Extract The full Information Matrix
information2.lme2 | Extract The full Information Matrix
information2.lvmfit | Extract The full Information Matrix
information2.lvmfit2 | Extract The full Information Matrix
initVarLink | Normalize var1 and var2
initVarLinks | Normalize var1 and var2
intDensTri | Integrate a Gaussian/Student Density over a Triangle

## -- L --

lavaSearch2 | Tools for Model Specification in the Latent Variable Framework
lavaSearch2, | Tools for Model Specification in the Latent Variable Framework
leverage2 | Extract Leverage Values
leverage2.gls | Extract Leverage Values
leverage2.gls2 | Extract Leverage Values
leverage2.lm | Extract Leverage Values
leverage2.lm2 | Extract Leverage Values
leverage2.lme | Extract Leverage Values
leverage2.lme2 | Extract Leverage Values
leverage2.lvmfit | Extract Leverage Values
leverage2.lvmfit2 | Extract Leverage Values

## -- M --

matrixPower | Power of a Matrix
modelsearch2 | Data-driven Extension of a Latent Variable Model
modelsearch2.lvmfit | Data-driven Extension of a Latent Variable Model

## -- N --

nStep | Find the Number of Steps Performed During the Sequential Testing
nStep.modelsearch2 | Find the Number of Steps Performed During the Sequential Testing

## -- R --

residuals2 | Extract Corrected Residuals
residuals2.gls2 | Extract Corrected Residuals
residuals2.lm2 | Extract Corrected Residuals
residuals2.lme2 | Extract Corrected Residuals
residuals2.lvmfit2 | Extract Corrected Residuals

## -- S --

score2 | Extract the Individual Score
score2.gls | Extract the Individual Score
score2.gls2 | Extract the Individual Score
score2.lm | Extract the Individual Score
score2.lm2 | Extract the Individual Score
score2.lme | Extract the Individual Score
score2.lme2 | Extract the Individual Score
score2.lvmfit | Extract the Individual Score
score2.lvmfit2 | Extract the Individual Score
sCorrect | Satterthwaite Correction and Small Sample Correction
sCorrect.gls | Satterthwaite Correction and Small Sample Correction
sCorrect.gls2 | Satterthwaite Correction and Small Sample Correction
sCorrect.lm | Satterthwaite Correction and Small Sample Correction
sCorrect.lm2 | Satterthwaite Correction and Small Sample Correction
sCorrect.lme | Satterthwaite Correction and Small Sample Correction
sCorrect.lme2 | Satterthwaite Correction and Small Sample Correction
sCorrect.lvmfit | Satterthwaite Correction and Small Sample Correction
sCorrect.lvmfit2 | Satterthwaite Correction and Small Sample Correction
sCorrect<- | Satterthwaite Correction and Small Sample Correction
sCorrect<-.gls | Satterthwaite Correction and Small Sample Correction
sCorrect<-.gls2 | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lm | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lm2 | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lme | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lme2 | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lvmfit | Satterthwaite Correction and Small Sample Correction
sCorrect<-.lvmfit2 | Satterthwaite Correction and Small Sample Correction
setLink | Set a Link to a Value
setLink.lvm | Set a Link to a Value
summary.calibrateType1 | Display the Type 1 Error Rate
summary.modelsearch2 | summary Method for modelsearch2 Objects
summary2 | Summary with Small Sample Correction
summary2.gls | Summary with Small Sample Correction
summary2.gls2 | Summary with Small Sample Correction
summary2.lm | Summary with Small Sample Correction
summary2.lm2 | Summary with Small Sample Correction
summary2.lme | Summary with Small Sample Correction
summary2.lme2 | Summary with Small Sample Correction
summary2.lvmfit | Summary with Small Sample Correction
summary2.lvmfit2 | Summary with Small Sample Correction

## -- T --

tryWithWarnings | Run an Expression and Catch Warnings and Errors

## -- V --

vcov2 | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.gls | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.gls2 | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lm | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lm2 | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lme | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lme2 | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lvmfit | Extract the Variance Covariance Matrix of the Model Parameters
vcov2.lvmfit2 | Extract the Variance Covariance Matrix of the Model Parameters

## -- misc --

.compare2 | Test Linear Hypotheses with small sample correction