All functions

By()

Apply a Function to a Data Frame Split by Factors

Col()

Generate a transparent RGB color

Combine()

Report estimates across different models

Expand()

Create a Data Frame from All Combinations of Factors

Graph() `Graph<-`()

Extract graph

Grep()

Finds elements in vector or column-names in data.frame/matrix

Missing()

Missing value generator

Model() `Model<-`()

Extract model

NA2x()

Convert to/from NA

NR()

Newton-Raphson method

PD()

Dose response calculation for binomial regression models

Range.lvm()

Define range constraints of parameters

addvar()

Add variable to (model) object

backdoor()

Backdoor criterion

baptize()

Label elements of object

binomial.rd()

Define constant risk difference or relative risk association for binary exposure

blockdiag()

Combine matrices to block diagonal structure

bmd

Longitudinal Bone Mineral Density Data (Wide format)

bmidata

Data

bootstrap()

Generic bootstrap method

bootstrap(<lvm>) bootstrap(<lvmfit>)

Calculate bootstrap estimates of a lvm object

brisa

Simulated data

calcium

Longitudinal Bone Mineral Density Data

cancel()

Generic cancel method

children()

Extract children or parent elements of object

click(<default>) idplot()

Identify points on plot

closed.testing()

Closed testing procedure

colorbar()

Add color-bar to plot

commutation()

Finds the unique commutation matrix

compare()

Statistical tests

complik()

Composite Likelihood for probit latent variable models

confband()

Add Confidence limits bar to plot

confint(<lvmfit>)

Calculate confidence limits for parameters

confpred()

Conformal prediction

`constrain<-`(<default>) `constrain<-`(<multigroup>) constraints()

Add non-linear constraints to latent variable model

contr()

Create contrast matrix

correlation()

Generic method for extracting correlation coefficients of model object

`covariance<-`(<lvm>)

Add covariance structure to Latent Variable Model

csplit()

Split data into folds

curly()

Adds curly brackets to plot

cv()

Cross-validation

devcoords()

Returns device-coordinates and plot-region

diagtest()

Calculate diagnostic tests for 2x2 table

dsep(<lvm>)

Check d-separation criterion

equivalence()

Identify candidates of equivalent models

estimate(<default>)

Estimation of functional of parameters

estimate(<lvm>)

Estimation of parameters in a Latent Variable Model (lvm)

eventTime()

Add an observed event time outcome to a latent variable model.

fplot()

fplot

getMplus()

Read Mplus output

getSAS()

Read SAS output

gof() moments() logLik(<lvmfit>) score(<lvmfit>) information(<lvmfit>)

Extract model summaries and GOF statistics for model object

hubble

Hubble data

hubble2

Hubble data

iid()

Extract i.i.d. decomposition (influence function) from model object

images()

Organize several image calls (for visualizing categorical data)

indoorenv

Data

`intercept<-`(<lvm>)

Fix mean parameters in 'lvm'-object

startvalues

For internal use

ksmooth2()

Plot/estimate surface

`labels<-`(<default>) `edgelabels<-`(<lvm>) `nodecolor<-`(<default>)

Define labels of graph

lava-package

Estimation and simulation of latent variable models

lava.options()

Set global options for lava

lvm()

Initialize new latent variable model

makemissing()

Create random missing data

measurement.error()

Two-stage (non-linear) measurement error

missingdata

Missing data example

mixture()

Estimate mixture latent variable model.

modelsearch()

Model searching

multinomial()

Estimate probabilities in contingency table

mvnmix()

Estimate mixture latent variable model

nldata

Example data (nonlinear model)

nsem

Example SEM data (nonlinear)

`%++%`

Concatenation operator

`%ni%`

Matching operator (x not in y) oposed to the %in%-operator (x in y)

`ordinal<-`()

Define variables as ordinal

ordreg()

Univariate cumulative link regression models

parpos()

Generic method for finding indeces of model parameters

partialcor()

Calculate partial correlations

path(<lvm>) effects(<lvmfit>)

Extract pathways in model graph

pcor()

Polychoric correlation

pdfconvert()

Convert pdf to raster format

plot(<estimate>)

Plot method for 'estimate' objects

plot(<lvm>)

Plot path diagram

plot(<sim>)

Plot method for simulation 'sim' objects

plotConf()

Plot regression lines

predict(<lvm>)

Prediction in structural equation models

predictlvm()

Predict function for latent variable models

rbind(<Surv>)

Appending Surv objects

regression(<lvm>) `regression<-`(<lvm>)

Add regression association to latent variable model

revdiag() offdiag() `revdiag<-`() `offdiag<-`()

Create/extract 'reverse'-diagonal matrix or off-diagonal elements

`rmvar<-`()

Remove variables from (model) object.

rotate2()

Performs a rotation in the plane

scheffe()

Calculate simultaneous confidence limits by Scheffe's method

semdata

Example SEM data

serotonin

Serotonin data

serotonin2

Data

sim(<lvm>)

Simulate model

sim(<default>)

Wrapper function for mclapply

spaghetti()

Spaghetti plot

stack(<estimate>)

Stack estimating equations

subset(<lvm>)

Extract subset of latent variable model

summary(<sim>)

Summary method for 'sim' objects

timedep()

Time-dependent parameters

toformula()

Converts strings to formula

tr()

Trace operator

trim()

Trim tring of (leading/trailing/all) white spaces

twindata

Twin menarche data

twostage()

Two-stage estimator

twostage(<lvmfit>)

Two-stage estimator (non-linear SEM)

twostageCV()

Cross-validated two-stage estimator

vars() endogenous() exogenous() manifest() latent() `exogenous<-`(<lvm>) `latent<-`(<lvm>)

Extract variable names from latent variable model

vec()

vec operator

wait()

Wait for user input (keyboard or mouse)

wkm()

Weighted K-means

wrapvec()

Wrap vector

zibreg()

Regression model for binomial data with unkown group of immortals