* Estimation and simulation of latent variable models

** Model building 

addvar                  Add variable to (model) object
adjMat			Extract adjancey matrix from model/graph
ancestors		Extract ancestors of nodes
baptize                 Label elements of object
cancel                  Generic cancel method
categorical		Define categorical variables (predictors)
children                Extract children or parent elements of object
constrain<-             Add non-linear constraints to latent variable model
covariance              Add covariance structure to Latent Variable Model
descendants		Extract descendants of nodes
describecoef		Show parameter names
edgeList		Extract edge list from model/graph
edgelabels		Define labels on edges of graph
eventTime               Add an observed event time outcome to a latent variable model.
fixsome			Constrain parameters in measurement models (identifiability)
functional		Add non-linear associations (for simulation only)
intercept               Fix mean parameters in 'lvm'-object
rmvar                   Remove variables from (model) object.
labels<-                Define labels of graph
lvm                     Initialize new latent variable model
makemissing             Create random missing data
measurement		Extract measurement models
merge			Merge model objects (lvm, estimate, ...)
multigroup		Define multiple group object
nodecolor		Set node colours
ordinal			Define variables as ordinal
parameter		Define additional parameters of the model
parpos                  Generic method for finding indeces of model parameters
parents			Extract parents of nodes
path                    Extract pathways in model graph
plot.lvm                Plot path diagram
Range.lvm               Define range constraints of parameters
regression<-            Add regression association to latent variable model
subset.lvm              Extract subset of latent variable model
timedep                 Time-dependent parameters
transform		Create non-linear parameter constraints
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
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
iid                     Extract i.i.d. decomposition (influence function) from model object
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
modelsearch             Model searching
moments			Estimate model-specific mean and variance
multinomial		Estimate probabilities in contingency table
nonlinear		Define non-linear associations (see 'twostage')
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
residuals		Extract residuals
riskcomp		Calculate association measure (see also 'OR','logor','Diff','Ratio')
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
startvalues             Starting values
twostage                Two-stage estimator (non-linear SEM)
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)
By                      Apply a Function to a Data Frame Split by Factors
click                   Identify points on plot
Col                     Generate a transparent RGB color
Combine                 Report estimates across different models
commutation             Finds the unique commutation matrix
csplit			Define random folds of data
curly			Add curly brackets to plot
dsort			Sort data.frame
Expand                  Create a Data Frame from All Combinations of Factors
fplot                   Faster plots of large data via rgl
getSAS			Read SAS output (ODS)
getMplus		Read Mplus output
Inverse			Generalized inverse			
ksmooth2		Estimate and visualize bivariate density 
PD                      Dose response calculation for binomial regression models
blockdiag               Combine matrices to block diagonal structure
colsel			Select colour(s) interactively
colorbar		Add colorbar to plot
confband                Add Confidence limits bar to plot
devcoords               Returns device-coordinates and plot-region
diagtest		Calculate diagnostic tests for 2x2 table
images                  Organize several image calls (for visualizing categorical data)
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
surface			Visualize function surface
offdiag			Extract or set off-diagonal elements of matrix
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

** Distributions

Missing			Add missing mechanism to model
normal.lvm		
lognormal.lvm
poisson.lvm		
threshold.lvm
binomial.lvm
Gamma.lvm
loggamma.lvm
chisq.lvm
student.lvm
uniform.lvm
weibull.lvm
sequence.lvm
ones.lvm
beta.lvm
GM2.lvm
GM3.lvm
coxWeibull.lvm
coxExponential.lvm
aalenExponential.lvm
coxGompertz.vlm
heavytail.lvm

** 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

