* 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<-            -
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<-             -
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<-             -
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<-            -
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

alpha_zmax              Multiple testing adjustment
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
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
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 simulated data
twindata                Twin menarche data
