* 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