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* Estimation and simulation of latent variable models
** Model building
addvar Add variable to (model) object
addvar<- -
adjMat Extract adjancey matrix from model/graph
ancestors Extract ancestors of nodes
baptize Label elements of object
cancel Remove assocation between variables
cancel<- -
categorical Define categorical variables (predictors)
categorical<- -
children Extract children or parent elements of object
constrain Add non-linear constraints to latent variable model
constrain<- -
covariance Add covariance structure to Latent Variable Model
covariance<- -
covfix -
covfix<- -
variance -
variance<- -
descendants Extract descendants of nodes
describecoef Show parameter names
distribution Define distribution of variables
distribution<- -
edgeList Extract edge list from model/graph
edgelabels Define labels on edges of graph
edgelabels<- -
edgeList Extract edges of 'lvm' object
endogenous Extract endogenous variables
exogenous Extract/define exogenous variables
exogenous<- -
eventTime Add an observed event time outcome to a latent variable model
eventTime<- -
fixsome Constrain parameters in measurement models (identifiability)
functional Add non-linear associations (for simulation only)
functional<- -
intercept Fix mean parameters in 'lvm'-object
intercept<- -
intfix -
intfix<- -
intervention Define intervention variable
intervention<- -
rmvar Remove variables from (model) object.
rmvar<- -
kill -
kill<- -
labels Define labels of graph
labels<- -
latent Define latent variable
latent<- -
lvm Initialize new latent variable model
makemissing Create random missing data
manifest Extract observed variables
measurement Extract measurement models
merge Merge model objects (lvm, estimate, ...)
multigroup Define multiple group object
nodecolor Set node colours
nodecolor<- -
ordinal Define variables as ordinal
ordinal<- -
parameter Define additional parameters of the model
parameter<- -
parfix Fix parameters of model
parfix<- -
parpos Generic method for finding indeces of model parameters
pars Extract model parameter names
parents Extract parents of nodes
path Extract pathways in model graph
plot.lvm Plot path diagram
Range.lvm Define range constraints of parameters
randomslope Define random slope component
randomslope<- -
regression Add regression association to latent variable model
regression<- -
regfix -
regfix<- -
roots Extract root nodes of graph
sinks Extract sink nodes of graph
subset.lvm Extract subset of latent variable model
timedep Time-dependent parameters
timedep<- -
transform Create non-linear parameter constraints
transform<- -
vars Extract variable names from latent variable model
** Model inference
backdoor Check backdoor criterion
bootstrap Generic bootstrap method
bootstrap.lvm Calculate bootstrap estimates of a lvm object
closed.testing Closed testing procedure
confint.lvmfit Calculate confidence limits for parameters
contr Create contrast matrices
compare Statistical tests Performs Likelihood-ratio, Wald and score tests
complik Composite likelihood inference
confpred Conformal prediction limits
correlation Generic method for extracting correlation coefficients of model object
cv Cross-validation function
dsep Check d-separation criterion in graph
equivalence Identify candidates of equivalent models
effects Mediation; calculate indirect, direct and total effects
totaleffects -
estimate.default Aggregation of parameters and data
estimate.lvm Estimation of parameters in a Latent Variable Model (lvm)
gof Extract model summaries and GOF statistics for model object
gkgamma Kruskal-Gamma for contigency tables
Graph Extract graph
Graph<- -
IC Extract i.i.d. decomposition (influence function) from model object
iid - (obsolete)
information Calculate information matrix
IV Instrumental variables estimator (2SLS)
kappa Cohens kappa
lava.options Set global options for 'lava'
measurement.error Two-stage estimator for (non-linear) measurement error models
Model Extract model
Model<- -
modelPar Extract model parameters
modelVar Extract variance structure
modelsearch Model searching
moments Estimate model-specific mean and variance
multinomial Estimate probabilities in contingency table
mvnmix Estimate multivariate normal mixture model
nonlinear Define non-linear associations (see 'twostage')
nonlinear<- -
ordreg Ordinal regression models
partialcor Calculate partial correlations
p.correct Multiple testing adjustment
pcor Polychoric correlations
plot.estimate Forest-plot or regression line plot
predict.lvm Prediction in structural equation models
profile Profile likelihood
mixture Estimate mixture latent variable model
residuals Extract residuals
riskcomp Calculate association measure (see also 'OR,'Diff','Ratio')
Diff -
OR -
Ratio -
odds -
expit -
logit -
tigol -
scheffe Simulatenous confidence bands (lm)
score Extract score function of model fit
stack.estimate Stack estimating equations
sim Simulate model
sim.default Wrapper function for mclapply
as.sim Cast matrix as 'sim' object
startvalues Starting values
starter.multigroup -
startvalues0 -
startvalues1 -
startvalues2 -
twostage Two-stage estimator (non-linear SEM)
twostageCV Cross-validation for non-linear SEM mixture models
wkm Weighted k-means algorithm
zibreg Regression model for binomial data with unknown group of unaffected
** Utilities
%++% Concatenation operator
%ni% Matching operator (x not in y) oposed to the '%in%'-operator (x in y)
blockdiag Combine matrices to block diagonal structure
By Apply a Function to a Data Frame Split by Factors
click Identify points on plot
wait -
Col Generate a transparent RGB color
Combine Report estimates across different models
commutation Finds the unique commutation matrix
csplit Define random folds of data
foldr -
curly Add curly brackets to plot
Expand Create a Data Frame from All Combinations of Factors
fplot Faster plots of large data via rgl
forestplot Forest plots (confidence/prediciton limits visualization)
getSAS Read SAS output (ODS)
getMplus Read Mplus output
ksmooth2 Estimate and visualize bivariate density
PD Dose response calculation for binomial regression models
colsel Select colour(s) interactively
colorbar Add colorbar to plot
confband Add Confidence limits bar to plot
plot_region -
devcoords Returns device-coordinates and plot-region
diagtest Calculate diagnostic tests for 2x2 table
images Organize several image calls (for visualizing categorical data)
Inverse Generalized inverse
org Convert object to ascii suitable for org-mode
parsedesign Create contrast matrix from expression
plotConf Plot regression lines
pdfconvert Convert pdf to raster format
procformula Process formula
revdiag Create/extract 'reverse'-diagonal matrix
revdiag<- -
surface Visualize function surface
offdiag Extract or set off-diagonal elements of matrix
offdiag<- -
density.sim Plot sim object
spaghetti Plot longitudinal data
toformula Converts strings to formula
tr Trace operator
trim Trim tring of (leading/trailing/all) white spaces
vec vec operator
wrapvec Wrap vector
x2NA Convert vector to/from NA
NA2x -
na.pass0 Handle missing data by setting NA to zero
** Distributions
Missing Add missing mechanism to model
Missing<- -
normal.lvm Normal distribution
gaussian.lvm -
lognormal.lvm Log-normal distribution
poisson.lvm Poisson distribution
threshold.lvm Threshold model (e.g., Probit)
binomial.lvm Binomial family / Bernoulli distribution
logit.lvm -
probit.lvm -
Gamma.lvm Gamma distribution
loggamma.lvm Log-Gamma distribution
chisq.lvm Chi-squared distribution
student.lvm Student-t distribution
uniform.lvm Uniform (continuous or discrete) distribution
weibull.lvm Weibull distribution
id.lvm Sequence of integers 1:n
Sequence.lvm -
ones.lvm Fixed sequence of zeros and ones
constant.lvm Fixed single value
binary.lvm -
Binary.lvm -
beta.lvm Beta distribution
multinomial.lvm Multinomial distribution
mvn.lvm Multivariate normal distribution
GM2.lvm Gaussian mixture distribution
GM3.lvm -
coxWeibull.lvm Cox-model (Weibull baseline)
coxExponential.lvm Cox-model (Exponential baseline)
coxGompertz.vlm Cox-model (Gompertz baseline)
aalenExponential.lvm Aalen additive model
heavytail.lvm Heavy-tailed distribution
heavytail<- -
binomial.rd Binomial odds-product model (risk difference)
binomial.rr Binomial odds-product model (relative risk)
pareto.lvm Pareto distribution
none.lvm Deterministic variable (fixed at its mean-structure)
** Datasets
bmd Longitudinal Bone Mineral Density Data (Wide format)
bmidata Data
brisa Simulated data
calcium Longitudinal Bone Mineral Density Data
hubble Hubble data
hubble2 Hubble data
indoorenv Data
nldata Example data (nonlinear model)
missingdata Data
nsem Example SEM data (nonlinear)
semdata Example SEM data
serotonin Serotonin data
serotonin2 Data
twindata Twin menarche data
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