Package: lava 1.9.2

lava: Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Authors:Klaus K. Holst [aut, cre], Benedikt Sommer [ctb], Brice Ozenne [ctb], Thomas Gerds [ctb]

lava_1.9.2.tar.gz
lava_1.9.2.zip(r-4.7)lava_1.9.2.zip(r-4.6)lava_1.9.2.zip(r-4.5)
lava_1.9.2.tgz(r-4.6-any)lava_1.9.2.tgz(r-4.5-any)
lava_1.9.2.tar.gz(r-4.7-any)lava_1.9.2.tar.gz(r-4.6-any)
lava_1.9.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
lava/json (API)
NEWS

# Install 'lava' in R:

install.packages('lava', repos = c('https://kkholst.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kkholst/lava/issues

Pkgdown/docs site:https://kkholst.github.io

Datasets:

bmd - Longitudinal Bone Mineral Density Data
bmidata - Data
brisa - Simulated data
calcium - Longitudinal Bone Mineral Density Data
deprdiag - 50 patients from Monash Medical Centre, Melbourne
hubble - Hubble data
hubble2 - Hubble data
indoorenv - Data
missingdata - Missing data example
nldata - Example data
nsem - Example SEM data
semdata - Example SEM data
serotonin - Serotonin data
twindata - Twin menarche data

On CRAN:

latent-variable-models simulation statistics structural-equation-models

15.62 score 33 stars 538 packages 807 scripts 179k downloads 4 mentions 248 exports 14 dependencies

Last updated from:8a9e16bd35. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	263
source / vignettes	OK	264
linux-release-x86_64	OK	234
macos-release-arm64	OK	150
macos-oldrel-arm64	OK	164
windows-devel	OK	236
windows-release	OK	226
windows-oldrel	OK	211
wasm-release	OK	149

Exports:%++%%in.closed%%in.open%%ni%aalenExponential.lvm addhook addvar addvar<-adjMat alpha_zmax ancestors as.sim backdoor baptize beta.lvm binary.lvm Binary.lvm binomial.lvm binomial.rd binomial.rr blockdiag bootstrap By cancel cancel<-categorical categorical<-children chisq.lvm click closed_testing CoefMat CoefMat.multigroupfit Col colorbar colsel Combine commutation compare complik confband confpred constant.lvm constrain constrain<-constraints contr correlation covariance covariance<-coxExponential.lvm coxGompertz.lvm coxWeibull.lvm csplit curly decomp.specials density.sim descendants describecoef devcoords diagtest Diff distribution distribution<-dmvn0 dsep edgelabels edgelabels<-edgeList endogenous equivalence estimate estimate.default eventTime eventTime<-exogenous exogenous<-Expand expit finalize fixsome foldr forestplot fplot functional functional<-Gamma.lvm gaussian_logLik.lvm gaussian.lvm gethook getoutcome getSAS gkgamma GM2.lvm GM3.lvm gof Graph Graph<-graph2lvm Grep heavytail heavytail<-IC id.lvm idplot igraph.lvm iid images index index<-information intercept intercept<-intervention intervention<-Inverse IV kill kill<-ksmooth2 labels<-latent latent<-lava lava.options loggamma.lvm logit logit.lvm lognormal.lvm lvm makemissing manifest mat.lvm measurement measurement.error Missing Missing<-mixture Model Model<-modelPar modelsearch modelVar moments multigroup multinomial multinomial.lvm mvn.lvm mvnmix na.pass0 NA2x nodecolor<-none.lvm nonlinear nonlinear<-normal.lvm NR odds offdiag offdiag<-offdiags ones.lvm OR ordinal ordinal<-ordreg pairwise.diff parameter parameter<-parents pareto.lvm parlabels parpos pars parsedesign partialcor path pcor PD pdfconvert plot_region plot.sim plotConf poisson.lvm predict_glm predictlvm Print probit.lvm procformula randomslope randomslope<-Range.lvm Ratio regfix regression regression<-revdiag revdiag<-riskcomp rmvar rmvar<-rmvn0 roots rot2D rot3D rotate2 rsq scheffe score Sequence.lvm sim sinks spaghetti Specials starter.multigroup startvalues startvalues0 startvalues1 startvalues2 student.lvm summary.sim surface test_wald threshold.lvm tigol timedep timedep<-toformula totaleffects tr transform<-trim twostage twostageCV uniform.lvm var_ic variance variance<-variances vars vec wait weibull.lvm Weights wkm wrapvec x2NA zibreg

Dependencies:cli codetools digest future future.apply globals lattice listenv Matrix numDeriv parallelly progressr SQUAREM survival

Estimating partial correlations with lava

Klaus Kähler Holst

Rendered fromcorrelation.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-03
Started: 2020-05-23

Non-linear latent variable models and error-in-variable models

Klaus Kähler Holst

Rendered fromnonlinear.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-02
Started: 2020-05-23

The Art of Influence

Klaus Kähler Holst

Rendered frominfluencefunction.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-05-11
Started: 2023-11-15

Help page	Topics
Concatenation operator	%++%
Matching operator (x not in y) oposed to the '%in%'-operator (x in y)	%in.closed% %in.open% %ni%
Add variable to (model) object	addvar addvar<-
Backdoor criterion	backdoor
Label elements of object	baptize
Define constant risk difference or relative risk association for binary exposure	binomial.rd binomial.rr
Combine matrices to block diagonal structure	blockdiag
Longitudinal Bone Mineral Density Data (Wide format)	bmd
Data	bmidata
Generic bootstrap method	bootstrap
Calculate bootstrap estimates of a lvm object	bootstrap.lvm bootstrap.lvmfit
Simulated data	brisa
Apply a Function to a Data Frame Split by Factors	By
Longitudinal Bone Mineral Density Data	calcium
Generic cancel method	cancel cancel<-
Extract children or parent elements of object	adjMat ancestors children descendants edgeList parents roots sinks
Identify points on plot	click click.default colsel idplot
Closed testing procedure	alpha_zmax closed_testing
Generate a transparent RGB color	Col
Add color-bar to plot	colorbar
Report estimates across different models	Combine
Finds the unique commutation matrix	commutation
Statistical tests	compare test_wald
Composite Likelihood for probit latent variable models	complik
Add Confidence limits bar to plot	confband forestplot plot_region
Calculate confidence limits for parameters	confint.lvmfit confint.multigroupfit
Conformal prediction	confpred
Add non-linear constraints to latent variable model	constrain constrain.default constrain<- constrain<-.default constrain<-.multigroup constraints parameter<-
Create contrast matrix	contr pairwise.diff parsedesign
Generic method for extracting correlation coefficients of model object	correlation
Add covariance structure to Latent Variable Model	covariance covariance.lvm covariance<- covariance<-.lvm variance variance.lvm variance<- variance<-.lvm
Split data into folds	csplit foldr
Adds curly brackets to plot	curly
50 patients from Monash Medical Centre, Melbourne	deprdiag
Returns device-coordinates and plot-region	devcoords
Calculate diagnostic tests for 2x2 table	diagtest Diff odds OR Ratio riskcomp
Check d-separation criterion	dsep dsep.lvm
Identify candidates of equivalent models	equivalence
Estimate parameters and influence function.	estimate.array estimate.data.frame
Influence function based inference	estimate estimate.default estimate.mlm merge.estimate
Estimation of parameters in a Latent Variable Model (lvm)	estimate.lvm
Add an observed event time outcome to a latent variable model.	eventTime eventTime<-
Create a Data Frame from All Combinations of Factors	Expand
fplot	fplot
Read SAS output	getSAS
Extract model summaries and GOF statistics for model object	gof gof.lvmfit information information.lvmfit logLik.lvmfit moments moments.lvm score score.lvmfit
Extract graph	Graph Graph<-
Finds elements in vector or column-names in data.frame/matrix	Grep
Hubble data	hubble
Hubble data	hubble2
Extract influence function from model object	IC IC.default var_ic
Extract i.i.d. decomposition from model object	iid
Organize several image calls (for visualizing categorical data)	images
Generic method for extract index of an object	index index<-
Extract the parameter indicies of a lvm object	index.lvm index.lvmfit index<-.lvm index<-.lvmfit
Data	indoorenv
Fix mean parameters in 'lvm'-object	intercept intercept.lvm intercept<- intercept<-.lvm
Define intervention	intervention intervention.lvm intervention<- intervention<-.lvm
Generalized matrix inverse	Inverse
Plot/estimate surface	ksmooth2 surface
Define labels of graph	edgelabels edgelabels<- edgelabels<-.lvm labels labels.graphNEL labels.lvm labels.lvmfit labels<- labels<-.default nodecolor nodecolor<- nodecolor<-.default
Set global options for 'lava'	lava.options
Initialize new latent variable model	lvm print.lvm summary.lvm
Create random missing data	makemissing
Two-stage (non-linear) measurement error	measurement.error
Missing value generator	Missing Missing, Missing<-
Missing data example	missingdata
Estimate mixture latent variable model.	mixture
Extract model	Model Model<-
Model searching	modelsearch
Estimate probabilities in contingency table	gkgamma kappa.multinomial kappa.table multinomial
Estimate mixture latent variable model	mvnmix
Handle Missing Values in Objects	na.pass0
Convert to/from NA	NA2x x2NA
Example data (nonlinear model)	nldata
Newton-Raphson method	NR
Example SEM data (nonlinear)	nsem
Define variables as ordinal	ordinal ordinal<-
Univariate cumulative link regression models	ordreg
Generic method for finding indeces of model parameters	parpos
Calculate partial correlations	partialcor
Extract pathways in model graph	effects effects.lvmfit path path.lvm totaleffects
Polychoric correlation	pcor
Dose response calculation for binomial regression models	PD
Convert pdf to raster format	pdfconvert
Plot method for 'estimate' objects	plot.estimate
Plot path diagram	plot.lvm plot.lvmfit
Plot method for simulation 'sim' objects	density.sim plot.sim
Plot regression lines	plotConf
Predict from a GLM with modified coefficients	predict_glm
Prediction in structural equation models	predict.lvm predict.lvmfit
Predict function for latent variable models	predictlvm
Generic print method	Print
Define range constraints of parameters	Range.lvm
Appending 'Surv' objects	rbind.Surv
Add regression association to latent variable model	regression regression.lvm regression<- regression<-.lvm
Create/extract 'reverse'-diagonal matrix or off-diagonal elements	offdiag offdiag<- revdiag revdiag<-
Remove variables from (model) object.	kill kill<- rmvar rmvar<-
Performs a rotation in the plane	rot2D rot3D rotate2
Calculate simultaneous confidence limits by Scheffe's method	scheffe
Example SEM data	semdata
Serotonin data	serotonin
Monte Carlo simulation	as.sim sim sim.default
Simulate model	aalenExponential.lvm beta.lvm Binary.lvm binary.lvm binomial.lvm categorical categorical<- chisq.lvm constant.lvm coxExponential.lvm coxGompertz.lvm coxWeibull.lvm distribution distribution.lvm distribution<- distribution<-.lvm functional functional.lvm functional<- functional<-.lvm Gamma.lvm gamma.lvm gaussian.lvm GM2.lvm GM3.lvm heavytail heavytail<- id.lvm loggamma.lvm logit.lvm lognormal.lvm multinomial.lvm mvn.lvm none.lvm normal.lvm ones.lvm pareto.lvm poisson.lvm probit.lvm Sequence.lvm sim.lvm sim.lvmfit simulate.lvm simulate.lvmfit student.lvm threshold.lvm transform.lvm transform<- transform<-.lvm uniform.lvm weibull.lvm
Spaghetti plot	spaghetti
Stack estimating equations	stack.estimate
Extract subset of latent variable model	measurement subset.lvm
Summary method for 'sim' objects	summary.sim
Time-dependent parameters	timedep timedep<-
Converts strings to formula	toformula
Trace operator	tr
Trim string of (leading/trailing/all) white spaces	trim
Twin menarche data	twindata
Two-stage estimator	twostage
Two-stage estimator (non-linear SEM)	nonlinear nonlinear<- twostage.estimate twostage.lvm twostage.lvm.mixture twostage.lvmfit
Cross-validated two-stage estimator	twostageCV
Extract variable names from latent variable model	endogenous endogenous.lvm endogenous.lvmfit endogenous.multigroup exogenous exogenous.lvm exogenous.lvmfit exogenous.multigroup exogenous<- exogenous<-.lvm latent latent.lvm latent.lvmfit latent.multigroup latent<- latent<-.lvm manifest manifest.lvm manifest.lvmfit manifest.multigroup vars vars.lvm vars.lvmfit
vec operator	vec
Wait for user input (keyboard or mouse)	wait waitclick
Weighted K-means	wkm
Wrap vector	wrapvec
Regression model for binomial data with unkown group of immortals	zibreg

Package: lava 1.9.2

lava: Latent Variable Models

Estimating partial correlations with lava

Non-linear latent variable models and error-in-variable models

The Art of Influence

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)