Latent Variable Models

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Documentation for package ‘lava’ version 1.7.2.1

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

lava-package Estimation and simulation of latent variable models

-- A --

aalenExponential.lvm Simulate model
addattr For internal use
addhook For internal use
addvar Add variable to (model) object
addvar<- Add variable to (model) object
adjMat Extract children or parent elements of object
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
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 --

calcium Longitudinal Bone Mineral Density Data
cancel Generic cancel method
cancel<- Generic cancel method
categorical Simulate model
categorical<- Simulate model
checkmultigroup For internal use
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
CoefMat For internal use
CoefMat.multigroupfit For internal use
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
covfix Add covariance structure to Latent Variable Model
covfix.lvm Add covariance structure to Latent Variable Model
covfix<- Add covariance structure to Latent Variable Model
covfix<-.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 --

decomp.specials For internal use
density.sim Plot method for simulation 'sim' objects
deriv For internal use
descendants Extract children or parent elements of object
describecoef For internal use
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
dmvn0 For internal use
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 Estimation of functional of parameters
estimate.default Estimation of functional of parameters
estimate.estimate Estimation of functional of parameters
estimate.lvm Estimation of parameters in a Latent Variable Model (lvm)
estimate.MAR For internal use
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
expit For internal use

-- F --

finalize For internal use
fixsome For internal use
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
gaussian_logLik.lvm For internal use
gethook For internal use
getMplus Read Mplus output
getoutcome For internal use
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
graph2lvm For internal use
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 i.i.d. decomposition (influence function) from model object
IC.default Extract i.i.d. decomposition (influence function) from model object
id.lvm Simulate model
Identical For internal use
idplot Identify points on plot
igraph.lvm For internal use
iid Extract i.i.d. decomposition from model object
images Organize several image calls (for visualizing categorical data)
index For internal use
index.lvm For internal use
index.lvmfit For internal use
index<- For internal use
indoorenv Data
information Extract model summaries and GOF statistics for model object
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
intfix Fix mean parameters in 'lvm'-object
intfix.lvm Fix mean parameters in 'lvm'-object
intfix<- Fix mean parameters in 'lvm'-object
intfix<-.lvm Fix mean parameters in 'lvm'-object
Inverse For internal use
IV For internal use

-- 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 Estimation and simulation of latent variable models
lava.options Set global options for 'lava'
lisrel For internal use
loggamma.lvm Simulate model
logit For internal use
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
matrices For internal use
measurement Extract subset of latent variable model
measurement.error Two-stage (non-linear) measurement error
merge For internal use
merge.estimate Estimation of functional of parameters
Missing Missing value generator
Missing, Missing value generator
Missing<- Missing value generator
missingdata Missing data example
missingModel For internal use
mixture Estimate mixture latent variable model.
Model Extract model
Model<- Extract model
modelPar For internal use
modelsearch Model searching
modelVar For internal use
moments Extract model summaries and GOF statistics for model object
moments.lvm Extract model summaries and GOF statistics for model object
multigroup For internal use
multinomial Estimate probabilities in contingency table
multinomial.lvm Simulate model
mvn.lvm Simulate model
mvnmix Estimate mixture latent variable model

-- N --

na.pass0 For internal use
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
offdiags For internal use
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 --

p.correct Closed testing procedure
pairwise.diff Create contrast matrix
parameter For internal use
parameter<- Add non-linear constraints to latent variable model
parents Extract children or parent elements of object
pareto.lvm Simulate model
parfix For internal use
parfix<- For internal use
parlabels For internal use
parpos Generic method for finding indeces of model parameters
pars For internal use
pars.glm For internal use
pars.lvm For internal use
pars.lvmfit For internal use
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
print.lvm Initialize new latent variable model
probit.lvm Simulate model
procdata.lvmfit For internal use
procformula For internal use
profci For internal use

-- R --

randomslope For internal use
randomslope<- For internal use
Range.lvm Define range constraints of parameters
Ratio Calculate diagnostic tests for 2x2 table
rbind.Surv Appending 'Surv' objects
regfix Add regression association to latent variable model
regfix.lvm Add regression association to latent variable model
regfix<- Add regression association to latent variable model
regfix<-.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
regression<- Add regression association to latent variable model
regression<-.lvm Add regression association to latent variable model
reindex For internal use
reorderdata For internal use
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.
rmvn0 For internal use
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
rsq For internal use

-- S --

scheffe Calculate simultaneous confidence limits by Scheffe's method
score Extract model summaries and GOF statistics for model object
score.glm For internal use
score.lvmfit Extract model summaries and GOF statistics for model object
semdata Example SEM data
Sequence.lvm Simulate model
serotonin Serotonin data
serotonin2 Data
sim Simulate model
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
Specials For internal use
stack.estimate Stack estimating equations
starter.multigroup For internal use
startvalues For internal use
startvalues0 For internal use
startvalues1 For internal use
startvalues2 For internal use
startvalues3 For internal use
stdcoef For internal use
student.lvm Simulate model
subgraph For internal use
subset.lvm Extract subset of latent variable model
summary.lvm Initialize new latent variable model
summary.sim Summary method for 'sim' objects
surface Plot/estimate surface

-- T --

threshold.lvm Simulate model
tigol For internal use
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
updatelvm For internal use

-- 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
variances For internal use
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 Extract i.i.d. decomposition (influence function) from model object
vec vec operator

-- W --

wait Wait for user input (keyboard or mouse)
waitclick Wait for user input (keyboard or mouse)
weibull.lvm Simulate model
Weights For internal use
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
%ni% Matching operator (x not in y) oposed to the '%in%'-operator (x in y)