# Latent Variable Models

## Documentation for package ‘lava’ version 1.9.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X Z misc

## -- A --

aalenExponential.lvm | Simulate model
addvar | Add variable to (model) object
addvar<- | Add variable to (model) object
adjMat | Extract children or parent elements of object
alpha_zmax | Closed testing procedure
ancestors | Extract children or parent elements of object
as.sim | Monte Carlo simulation

## -- B --

backdoor | Backdoor criterion
baptize | Label elements of object
beta.lvm | Simulate model
binary.lvm | Simulate model
binomial.lvm | Simulate model
binomial.rd | Define constant risk difference or relative risk association for binary exposure
binomial.rr | 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 | Calculate bootstrap estimates of a lvm object
bootstrap.lvmfit | Calculate bootstrap estimates of a lvm object
brisa | Simulated data
By | Apply a Function to a Data Frame Split by Factors

## -- C --

c.estimate | Concatenate estimate objects
c.summary.estimate | Concatenate summary.estimate objects
calcium | Longitudinal Bone Mineral Density Data
cancel | Generic cancel method
cancel<- | Generic cancel method
categorical | Simulate model
categorical<- | Simulate model
children | Extract children or parent elements of object
chisq.lvm | Simulate model
click | Identify points on plot
click.default | Identify points on plot
closed_testing | Closed testing procedure
Col | Generate a transparent RGB color
colorbar | Add color-bar to plot
colsel | Identify points on plot
Combine | Report estimates across different models
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
confint.multigroupfit | Calculate confidence limits for parameters
confpred | Conformal prediction
constant.lvm | Simulate model
constrain | Add non-linear constraints to latent variable model
constrain.default | Add non-linear constraints to latent variable model
constrain<- | Add non-linear constraints to latent variable model
constrain<-.default | Add non-linear constraints to latent variable model
constrain<-.multigroup | Add non-linear constraints to latent variable model
constraints | Add non-linear constraints to latent variable model
contr | Create contrast matrix
correlation | Generic method for extracting correlation coefficients of model object
covariance | Add covariance structure to Latent Variable Model
covariance.lvm | Add covariance structure to Latent Variable Model
covariance<- | Add covariance structure to Latent Variable Model
covariance<-.lvm | Add covariance structure to Latent Variable Model
coxExponential.lvm | Simulate model
coxGompertz.lvm | Simulate model
coxWeibull.lvm | Simulate model
csplit | Split data into folds
curly | Adds curly brackets to plot

## -- D --

density.sim | Plot method for simulation 'sim' objects
deprdiag | 50 patients from Monash Medical Centre, Melbourne
descendants | Extract children or parent elements of object
devcoords | Returns device-coordinates and plot-region
diagtest | Calculate diagnostic tests for 2x2 table
Diff | Calculate diagnostic tests for 2x2 table
distribution | Simulate model
distribution.lvm | Simulate model
distribution<- | Simulate model
distribution<-.lvm | Simulate model
dist_aalen_exponential | Simulate model
dist_bernoulli | Simulate model
dist_beta | Simulate model
dist_chisq | Simulate model
dist_const | Simulate model
dist_cox_exponential | Simulate model
dist_cox_gompertz | Simulate model
dist_cox_weibull | Simulate model
dist_gamma | Simulate model
dist_gaussian | Simulate model
dist_gaussian_mixture2 | Simulate model
dist_gaussian_mixture3 | Simulate model
dist_loggamma | Simulate model
dist_lognormal | Simulate model
dist_multinomial | Simulate model
dist_mvn | Simulate model
dist_none | Simulate model
dist_ones | Simulate model
dist_pareto | Simulate model
dist_poisson | Simulate model
dist_seq | Simulate model
dist_seqint | Simulate model
dist_t | Simulate model
dist_threshold | Simulate model
dist_uniform | Simulate model
dist_weibull | Simulate model
dsep | Check d-separation criterion
dsep.lvm | Check d-separation criterion

## -- E --

edgelabels | Define labels of graph
edgelabels<- | Define labels of graph
edgelabels<-.lvm | Define labels of graph
edgeList | Extract children or parent elements of object
effects | Extract pathways in model graph
effects.lvmfit | Extract pathways in model graph
endogenous | Extract variable names from latent variable model
endogenous.lvm | Extract variable names from latent variable model
endogenous.lvmfit | Extract variable names from latent variable model
endogenous.multigroup | Extract variable names from latent variable model
equivalence | Identify candidates of equivalent models
estimate | Influence function based inference
estimate.array | Estimate parameters and influence function.
estimate.data.frame | Estimate parameters and influence function.
estimate.default | Influence function based inference
estimate.formula | Estimate method for formulas
estimate.glm | Estimate method for GLM objects
estimate.list | Estimate method for lists
estimate.lvm | Estimation of parameters in a Latent Variable Model (lvm)
estimate.mlm | Influence function based inference
eventTime | Add an observed event time outcome to a latent variable model.
eventTime<- | Add an observed event time outcome to a latent variable model.
exogenous | Extract variable names from latent variable model
exogenous.lvm | Extract variable names from latent variable model
exogenous.lvmfit | Extract variable names from latent variable model
exogenous.multigroup | Extract variable names from latent variable model
exogenous<- | Extract variable names from latent variable model
exogenous<-.lvm | Extract variable names from latent variable model
Expand | Create a Data Frame from All Combinations of Factors

## -- F --

foldr | Split data into folds
forestplot | Add Confidence limits bar to plot
fplot | fplot
functional | Simulate model
functional.lvm | Simulate model
functional<- | Simulate model
functional<-.lvm | Simulate model

## -- G --

Gamma.lvm | Simulate model
gamma.lvm | Simulate model
gaussian.lvm | Simulate model
getSAS | Read SAS output
gkgamma | Estimate probabilities in contingency table
GM2.lvm | Simulate model
GM3.lvm | Simulate model
gof | Extract model summaries and GOF statistics for model object
gof.lvmfit | Extract model summaries and GOF statistics for model object
Graph | Extract graph
Graph<- | Extract graph
Grep | Finds elements in vector or column-names in data.frame/matrix

## -- H --

heavytail | Simulate model
heavytail<- | Simulate model
hubble | Hubble data
hubble2 | Hubble data

## -- I --

IC | Extract influence function from model object
IC.default | Extract influence function from model object
id.lvm | Simulate model
idplot | Identify points on plot
iid | Extract i.i.d. decomposition from model object
images | Organize several image calls (for visualizing categorical data)
index | Generic method for extract index of an object
index.lvm | Extract the parameter indicies of a lvm object
index.lvmfit | Extract the parameter indicies of a lvm object
index<- | Generic method for extract index of an object
index<-.lvm | Extract the parameter indicies of a lvm object
index<-.lvmfit | Extract the parameter indicies of a lvm object
indoorenv | Data
information | Extract information matrix
information.lvmfit | Extract model summaries and GOF statistics for model object
intercept | Fix mean parameters in 'lvm'-object
intercept.lvm | Fix mean parameters in 'lvm'-object
intercept<- | Fix mean parameters in 'lvm'-object
intercept<-.lvm | Fix mean parameters in 'lvm'-object
intervention | Define intervention
intervention.lvm | Define intervention
intervention<- | Define intervention
intervention<-.lvm | Define intervention
Inverse | Generalized matrix inverse

## -- K --

kappa.multinomial | Estimate probabilities in contingency table
kappa.table | Estimate probabilities in contingency table
kill | Remove variables from (model) object.
kill<- | Remove variables from (model) object.
ksmooth2 | Plot/estimate surface

## -- L --

labels | Define labels of graph
labels.graphNEL | Define labels of graph
labels.lvm | Define labels of graph
labels.lvmfit | Define labels of graph
labels<- | Define labels of graph
labels<-.default | Define labels of graph
latent | Extract variable names from latent variable model
latent.lvm | Extract variable names from latent variable model
latent.lvmfit | Extract variable names from latent variable model
latent.multigroup | Extract variable names from latent variable model
latent<- | Extract variable names from latent variable model
latent<-.lvm | Extract variable names from latent variable model
lava.options | Set global options for 'lava'
loggamma.lvm | Simulate model
logit.lvm | Simulate model
logLik.lvmfit | Extract model summaries and GOF statistics for model object
lognormal.lvm | Simulate model
lvm | Initialize new latent variable model

## -- M --

makemissing | Create random missing data
manifest | Extract variable names from latent variable model
manifest.lvm | Extract variable names from latent variable model
manifest.lvmfit | Extract variable names from latent variable model
manifest.multigroup | Extract variable names from latent variable model
measurement | Extract subset of latent variable model
measurement.error | Two-stage (non-linear) measurement error
measurement_error | Two-stage (non-linear) measurement error
merge.estimate | Merge estimate objects
Missing | Missing value generator
Missing, | Missing value generator
Missing<- | Missing value generator
missingdata | Missing data example
mixture | Estimate mixture latent variable model.
Model | Extract model
Model<- | Extract model
modelsearch | Model searching
moments | Extract model summaries and GOF statistics for model object
moments.lvm | Extract model summaries and GOF statistics for model object
multinomial | Estimate probabilities in contingency table
multinomial.lvm | Simulate model
mvn.lvm | Simulate model
mvnmix | Estimate mixture latent variable model

## -- N --

na.pass0 | Handle Missing Values in Objects
NA2x | Convert to/from NA
nldata | Example data (nonlinear model)
nodecolor | Define labels of graph
nodecolor<- | Define labels of graph
nodecolor<-.default | Define labels of graph
none.lvm | Simulate model
nonlinear | Two-stage estimator (non-linear SEM)
nonlinear<- | Two-stage estimator (non-linear SEM)
normal.lvm | Simulate model
NR | Newton-Raphson method
nsem | Example SEM data (nonlinear)

## -- O --

odds | Calculate diagnostic tests for 2x2 table
offdiag | Create/extract 'reverse'-diagonal matrix or off-diagonal elements
offdiag<- | Create/extract 'reverse'-diagonal matrix or off-diagonal elements
ones.lvm | Simulate model
OR | Calculate diagnostic tests for 2x2 table
ordinal | Define variables as ordinal
ordinal<- | Define variables as ordinal
ordreg | Univariate cumulative link regression models

## -- P --

pairwise.diff | Create contrast matrix
pairwise_diff | Create contrast matrix
parameter<- | Add non-linear constraints to latent variable model
parents | Extract children or parent elements of object
pareto.lvm | Simulate model
parpos | Generic method for finding indeces of model parameters
parsedesign | Create contrast matrix
partialcor | Calculate partial correlations
path | Extract pathways in model graph
path.lvm | Extract pathways in model graph
pcor | Polychoric correlation
PD | Dose response calculation for binomial regression models
pdfconvert | Convert pdf to raster format
plot.estimate | Plot method for 'estimate' objects
plot.lvm | Plot path diagram
plot.lvmfit | Plot path diagram
plot.sim | Plot method for simulation 'sim' objects
plotConf | Plot regression lines
plot_region | Add Confidence limits bar to plot
poisson.lvm | Simulate model
predict.lvm | Prediction in structural equation models
predict.lvmfit | Prediction in structural equation models
predictlvm | Predict function for latent variable models
predict_glm | Predict from a GLM with modified coefficients
Print | Generic print method
print.lvm | Initialize new latent variable model
probit.lvm | Simulate model

## -- R --

Range.lvm | Define range constraints of parameters
Ratio | Calculate diagnostic tests for 2x2 table
rbind.Surv | Appending 'Surv' objects
regression | Add regression association to latent variable model
regression.lvm | Add regression association to latent variable model
regression<- | Add regression association to latent variable model
regression<-.lvm | Add regression association to latent variable model
revdiag | Create/extract 'reverse'-diagonal matrix or off-diagonal elements
revdiag<- | Create/extract 'reverse'-diagonal matrix or off-diagonal elements
riskcomp | Calculate diagnostic tests for 2x2 table
rmvar | Remove variables from (model) object.
rmvar<- | Remove variables from (model) object.
roots | Extract children or parent elements of object
rot2D | Performs a rotation in the plane
rot3D | Performs a rotation in the plane
rotate2 | Performs a rotation in the plane

## -- S --

scheffe | Calculate simultaneous confidence limits by Scheffe's method
score | Extract score function
score.lvmfit | Extract model summaries and GOF statistics for model object
semdata | Example SEM data
Sequence.lvm | Simulate model
serotonin | Serotonin data
sim | Monte Carlo simulation
sim.default | Monte Carlo simulation
sim.lvm | Simulate model
sim.lvmfit | Simulate model
simulate.lvm | Simulate model
simulate.lvmfit | Simulate model
sinks | Extract children or parent elements of object
spaghetti | Spaghetti plot
stack.estimate | Stack estimating equations
student.lvm | Simulate model
subset.lvm | Extract subset of latent variable model
summary.estimate | Summary of estimate objects
summary.lvm | Initialize new latent variable model
summary.sim | Summary method for 'sim' objects
surface | Plot/estimate surface

## -- T --

test_wald | Statistical tests
threshold.lvm | Simulate model
timedep | Time-dependent parameters
timedep<- | Time-dependent parameters
toformula | Converts strings to formula
totaleffects | Extract pathways in model graph
tr | Trace operator
transform.lvm | Simulate model
transform<- | Simulate model
transform<-.lvm | Simulate model
trim | Trim string of (leading/trailing/all) white spaces
twindata | Twin menarche data
twostage | Two-stage estimator
twostage.estimate | Two-stage estimator (non-linear SEM)
twostage.lvm | Two-stage estimator (non-linear SEM)
twostage.lvm.mixture | Two-stage estimator (non-linear SEM)
twostage.lvmfit | Two-stage estimator (non-linear SEM)
twostageCV | Cross-validated two-stage estimator

## -- U --

uniform.lvm | Simulate model

## -- V --

variance | Add covariance structure to Latent Variable Model
variance.lvm | Add covariance structure to Latent Variable Model
variance<- | Add covariance structure to Latent Variable Model
variance<-.lvm | Add covariance structure to Latent Variable Model
vars | Extract variable names from latent variable model
vars.lvm | Extract variable names from latent variable model
vars.lvmfit | Extract variable names from latent variable model
var_ic | Variance based on influence function
vec | vec operator

## -- W --

wait | Wait for user input (keyboard or mouse)
waitclick | Wait for user input (keyboard or mouse)
weibull.lvm | Simulate model
wkm | Weighted K-means
wrapvec | Wrap vector

## -- X --

x2NA | Convert to/from NA

## -- Z --

zibreg | Regression model for binomial data with unkown group of immortals

## -- misc --

%++% | Concatenation operator
%in.closed% | Matching operator (x not in y) oposed to the '%in%'-operator (x in y)
%in.open% | Matching operator (x not in y) oposed to the '%in%'-operator (x in y)
%ni% | Matching operator (x not in y) oposed to the '%in%'-operator (x in y)