lava: Latent Variable Models

Estimation and simulation of latent variable models.

AuthorKlaus K. Holst [aut, cre], Brice Ozenne [ctb], Thomas Gerds [ctb]
Date of publication2017-03-16 22:51:43 UTC
MaintainerKlaus K. Holst <klaus@holst.it>
LicenseGPL-3
Version1.5
https://github.com/kkholst/lava

View on CRAN

Man pages

addvar: Add variable to (model) object

backdoor: Backdoor criterion

baptize: Label elements of object

blockdiag: Combine matrices to block diagonal structure

bmd: Longitudinal Bone Mineral Density Data (Wide format)

bmidata: Data

bootstrap: Generic bootstrap method

bootstrap.lvm: Calculate bootstrap estimates of a lvm object

brisa: Simulated data

By: Apply a Function to a Data Frame Split by Factors

calcium: Longitudinal Bone Mineral Density Data

cancel: Generic cancel method

children: Extract children or parent elements of object

click: Identify points on plot

closed.testing: Closed testing procedure

Col: Generate a transparent RGB color

colorbar: Add color-bar to plot

Combine: Report estimates across different models

commutation: Finds the unique commutation matrix

compare: Statistical tests

complik: Composite Likelihood for probit latent variable models

confband: Add Confidence limits bar to plot

confint.lvmfit: Calculate confidence limits for parameters

constrain-set: Add non-linear constraints to latent variable model

contr: Create contrast matrix

correlation: Generic method for extracting correlation coefficients of...

covariance: Add covariance structure to Latent Variable Model

density.sim: Plot sim object

devcoords: Returns device-coordinates and plot-region

diagtest: Calculate diagnostic tests for 2x2 table

dsep.lvm: Check d-separation criterion

equivalence: Identify candidates of equivalent models

estimate.default: Estimation of functional of parameters

estimate.lvm: Estimation of parameters in a Latent Variable Model (lvm)

eventTime: Add an observed event time outcome to a latent variable...

Expand: Create a Data Frame from All Combinations of Factors

fplot: fplot

getMplus: Read Mplus output

getSAS: Read SAS output

gof: Extract model summaries and GOF statistics for model object

Graph: Extract graph

hubble: Hubble data

hubble2: Hubble data

iid: Extract i.i.d. decomposition (influence function) from model...

images: Organize several image calls (for visualizing categorical...

indoorenv: Data

intercept: Fix mean parameters in 'lvm'-object

internal: For internal use

kill: Remove variables from (model) object.

ksmooth2: Plot/estimate surface

labels-set: Define labels of graph

lava.options: Set global options for 'lava'

lava-package: Estimation and simulation of latent variable models

lvm: Initialize new latent variable model

makemissing: Create random missing data

measurement.error: Two-stage (non-linear) measurement error

Missing: Missing value generator

missingdata: Missing data example

Model: Extract model

modelsearch: Model searching

multinomial: Estimate probabilities in contingency table

nldata: Example data (nonlinear model)

nsem: Example SEM data (nonlinear)

op_concat: Concatenation operator

op_match: Matching operator (x not in y) oposed to the '%in%'-operator...

ordreg: Univariate cumulative link regression models

org: Convert object to ascii suitable for org-mode

parpos: Generic method for finding indeces of model parameters

partialcor: Calculate partial correlations

path: Extract pathways in model graph

pcor: Polychoric correlation

PD: Dose response calculation for binomial regression models

pdfconvert: Convert pdf to raster format

plotConf: Plot regression lines

plot.lvm: Plot path diagram

predictlvm: Predict function for latent variable models

predict.lvm: Prediction in structural equation models

Range.lvm: Define range constraints of parameters

regression-set: Add regression association to latent variable model

revdiag: Create/extract 'reverse'-diagonal matrix or off-diagonal...

scheffe: Calculate simultaneous confidence limits by Scheffe's method

semdata: Example SEM data

serotonin: Serotonin data

serotonin2: Data

sim: Simulate model

sim.default: Wrapper function for mclapply

spaghetti: Spaghetti plot

stack.estimate: Stack estimating equations

subset.lvm: Extract subset of latent variable model

timedep: Time-dependent parameters

toformula: Converts strings to formula

tr: Trace operator

trim: Trim tring of (leading/trailing/all) white spaces

twindata: Twin menarche data

twostage: Two-stage estimator

twostage.lvmfit: Two-stage estimator (non-linear SEM)

vars: Extract variable names from latent variable model

vec: vec operator

wrapvec: Wrap vector

zibreg: Regression model for binomial data with unkown group of...

Functions

\%++\% Man page
aalenExponential.lvm Man page
addattr Man page
addhook Man page
addvar Man page
addvar<- Man page
adjMat Man page
ancestors Man page
backdoor Man page
baptize Man page
beta.lvm Man page
binomial.lvm Man page
blockdiag Man page
bmd Man page
bmidata Man page
bootstrap Man page
bootstrap.lvm Man page
bootstrap.lvmfit Man page
brisa Man page
By Man page
calcium Man page
cancel Man page
cancel<- Man page
categorical Man page
categorical<- Man page
checkmultigroup Man page
children Man page
chisq.lvm Man page
click Man page
click.default Man page
closed.testing Man page
CoefMat Man page
CoefMat.multigroupfit Man page
Col Man page
colorbar Man page
Combine Man page
commutation Man page
compare Man page
complik Man page
confband Man page
confint.lvmfit Man page
confint.multigroupfit Man page
constrain Man page
constrain<- Man page
constrain<-.default Man page
constrain.default Man page
constrain<-.multigroup Man page
constraints Man page
contr Man page
correlation Man page
covariance Man page
covariance<- Man page
covariance<-.lvm Man page
covariance.lvm Man page
covfix Man page
covfix<- Man page
covfix<-.lvm Man page
covfix.lvm Man page
coxExponential.lvm Man page
coxGompertz.lvm Man page
coxWeibull.lvm Man page
decomp.specials Man page
density.sim Man page
deriv Man page
descendants Man page
describecoef Man page
devcoords Man page
diagtest Man page
Diff Man page
distribution Man page
distribution<- Man page
distribution<-.lvm Man page
distribution.lvm Man page
dmvn Man page
dsep Man page
dsep.lvm Man page
edgelabels Man page
edgelabels<- Man page
edgelabels<-.lvm Man page
edgeList Man page
effects Man page
effects.lvmfit Man page
endogenous Man page
endogenous.lvm Man page
endogenous.lvmfit Man page
endogenous.multigroup Man page
equivalence Man page
estimate Man page
estimate.default Man page
estimate.estimate Man page
estimate.lvm Man page
estimate.MAR Man page
eventTime Man page
eventTime<- Man page
exogenous Man page
exogenous<- Man page
exogenous<-.lvm Man page
exogenous.lvm Man page
exogenous.lvmfit Man page
exogenous.multigroup Man page
Expand Man page
expit Man page
finalize Man page
fixsome Man page
forestplot Man page
fplot Man page
functional Man page
functional<- Man page
functional<-.lvm Man page
functional.lvm Man page
gamma.lvm Man page
Gamma.lvm Man page
gaussian_logLik.lvm Man page
gaussian.lvm Man page
gethook Man page
getMplus Man page
getoutcome Man page
getSAS Man page
gkgamma Man page
GM2.lvm Man page
GM3.lvm Man page
gof Man page
gof.lvmfit Man page
Graph Man page
Graph<- Man page
graph2lvm Man page
heavytail Man page
heavytail<- Man page
hubble Man page
hubble2 Man page
idplot Man page
igraph.lvm Man page
iid Man page
iid.default Man page
images Man page
index Man page
index<- Man page
index.lvm Man page
index.lvmfit Man page
indoorenv Man page
information Man page
information.lvmfit Man page
intercept Man page
intercept<- Man page
intercept<-.lvm Man page
intercept.lvm Man page
intfix Man page
intfix<- Man page
intfix<-.lvm Man page
intfix.lvm Man page
Inverse Man page
IV Man page
kappa.multinomial Man page
kappa.table Man page
kill Man page
kill<- Man page
ksmooth2 Man page
labels Man page
labels<- Man page
labels<-.default Man page
labels.graphNEL Man page
labels.lvm Man page
labels.lvmfit Man page
latent Man page
latent<- Man page
latent<-.lvm Man page
latent.lvm Man page
latent.lvmfit Man page
latent.multigroup Man page
lava Man page
lava.options Man page
lava-package Man page
lisrel Man page
loggamma.lvm Man page
logit Man page
logit.lvm Man page
logLik.lvmfit Man page
lognormal.lvm Man page
lvm Man page
makemissing Man page
manifest Man page
manifest.lvm Man page
manifest.lvmfit Man page
manifest.multigroup Man page
matrices Man page
measurement Man page
measurement.error Man page
merge Man page
merge.estimate Man page
Missing Man page
Missing<- Man page
Missing, Man page
missingdata Man page
missingModel Man page
Model Man page
Model<- Man page
modelPar Man page
modelsearch Man page
modelVar Man page
moments Man page
moments.lvm Man page
multigroup Man page
multinomial Man page
\%ni\% Man page
nldata Man page
nodecolor Man page
nodecolor<- Man page
nodecolor<-.default Man page
normal.lvm Man page
NR Man page
nsem Man page
odds Man page
offdiag Man page
offdiag<- Man page
offdiags Man page
ones.lvm Man page
OR Man page
ordinal Man page
ordinal<- Man page
ordreg Man page
org Man page
parameter Man page
parameter<- Man page
parents Man page
pareto.lvm Man page
parfix Man page
parfix<- Man page
parlabels Man page
parpos Man page
pars Man page
parsedesign Man page
pars.glm Man page
pars.lvm Man page
pars.lvmfit Man page
partialcor Man page
path Man page
path.lvm Man page
pcor Man page
p.correct Man page
PD Man page
pdfconvert Man page
plotConf Man page
plot.lvm Man page
plot.lvmfit Man page
plot.sim Man page
poisson.lvm Man page
predictlvm Man page
predict.lvm Man page
predict.lvmfit Man page
print.lvm Man page
probit.lvm Man page
procdata.lvmfit Man page
procformula Man page
profci Man page
randomslope Man page
randomslope<- Man page
Range.lvm Man page
Ratio Man page
regfix Man page
regfix<- Man page
regfix<-.lvm Man page
regfix.lvm Man page
regression Man page
regression<- Man page
regression<-.lvm Man page
regression.lvm Man page
reindex Man page
reorderdata Man page
revdiag Man page
revdiag<- Man page
riskcomp Man page
rmvar Man page
rmvar<- Man page
rmvn Man page
roots Man page
rsq Man page
scheffe Man page
score Man page
score.glm Man page
score.lvmfit Man page
semdata Man page
sequence.lvm Man page
serotonin Man page
serotonin2 Man page
sim Man page
sim.default Man page
sim.lvm Man page
sim.lvmfit Man page
simulate.lvm Man page
simulate.lvmfit Man page
sinks Man page
spaghetti Man page
Specials Man page
stack.estimate Man page
starter.multigroup Man page
startvalues Man page
startvalues0 Man page
startvalues1 Man page
startvalues2 Man page
startvalues3 Man page
stdcoef Man page
student.lvm Man page
subgraph Man page
subset.lvm Man page
summary.lvm Man page
summary.sim Man page
surface Man page
survival Man page
survival<- Man page
threshold.lvm Man page
tigol Man page
timedep Man page
timedep<- Man page
toformula Man page
totaleffects Man page
tr Man page
transform<- Man page
transform<-.lvm Man page
transform.lvm Man page
trim Man page
twindata Man page
twostage Man page
twostage.estimate Man page
twostage.lvm Man page
twostage.lvmfit Man page
twostage.lvm.mixture Man page
uniform.lvm Man page
updatelvm Man page
variance Man page
variance<- Man page
variance<-.lvm Man page
variance.lvm Man page
variances Man page
vars Man page
vars.lvm Man page
vars.lvmfit Man page
vec Man page
weibull.lvm Man page
Weights Man page
wrapvec Man page
zibreg Man page

Files

lava
lava/inst
lava/inst/CITATION
lava/inst/gof1.png
lava/inst/lava1.png
lava/inst/mediation1.png
lava/inst/doc
lava/inst/doc/reference.pdf
lava/inst/me1.png
lava/inst/mediation2.png
lava/tests
lava/tests/testthat
lava/tests/testthat/test-model.R
lava/tests/testthat/test-estimate_default.R
lava/tests/testthat/test-sim.R
lava/tests/testthat/test-inference.R
lava/tests/testthat/test-constrain.R
lava/tests/testthat/test-multigroup.R
lava/tests/testthat/test-plot.R
lava/tests/testthat/test-graph.R
lava/tests/testthat/test-misc.R
lava/tests/test-all.R
lava/NAMESPACE
lava/demo
lava/demo/estimation.R
lava/demo/model.R
lava/demo/simulation.R
lava/demo/inference.R
lava/demo/00Index
lava/demo/lava.R
lava/NEWS
lava/data
lava/data/nldata.rda
lava/data/missingdata.rda
lava/data/nsem.rda
lava/data/semdata.rda
lava/data/serotonin.rda
lava/data/hubble.rda
lava/data/indoorenv.rda
lava/data/calcium.rda
lava/data/hubble2.rda
lava/data/bmidata.rda
lava/data/bmd.rda
lava/data/brisa.rda
lava/data/twindata.rda
lava/data/serotonin2.rda
lava/R
lava/R/categorical.R lava/R/equivalence.R lava/R/describecoef.R lava/R/nodecolor.R lava/R/onload.R lava/R/iid.R lava/R/parsedesign.R lava/R/zgetsas.R lava/R/cluster.hook.R lava/R/pdfconvert.R lava/R/utils.R lava/R/multipletesting.R lava/R/assoc.R lava/R/bootstrap.R lava/R/finalize.R lava/R/combine.R lava/R/operators.R lava/R/subset.R lava/R/randomslope.R lava/R/children.R lava/R/makemissing.R lava/R/covariance.R lava/R/matrices.R lava/R/multigroup.R lava/R/logLik.R lava/R/index.sem.R lava/R/regression.R lava/R/pars.R lava/R/model.R lava/R/endogenous.R lava/R/scheffe.R lava/R/confband.R lava/R/lmers.R lava/R/ordinal.R lava/R/plot.estimate.R lava/R/vcov.R lava/R/moments.R lava/R/plot.R lava/R/modelVar.R lava/R/zorg.R lava/R/devcoords.R lava/R/formula.R lava/R/startvalues.R lava/R/predict.R lava/R/logo.R lava/R/blockdiag.R lava/R/Col.R lava/R/profile.R lava/R/score.R lava/R/fplot.R lava/R/estimate.lvm.R lava/R/zib.R lava/R/addhook.R lava/R/variances.R lava/R/img.R lava/R/parpos.R lava/R/multinomial.R lava/R/glmest.R lava/R/revdiag.R lava/R/estimate.default.R lava/R/latent.R lava/R/estimate.multigroup.R lava/R/effects.R lava/R/plotConf.R lava/R/wrapvec.R lava/R/Missing.R lava/R/coef.R lava/R/weights.R lava/R/By.R lava/R/graph.R lava/R/iv.R lava/R/functional.R lava/R/kappa.R lava/R/contr.R lava/R/normal.R lava/R/path.R lava/R/interactive.R lava/R/score.survreg.R lava/R/lvm.R lava/R/Objective.R lava/R/commutation.R lava/R/print.R lava/R/sim.default.R lava/R/addattr.R lava/R/Expand.R lava/R/eventTime.R lava/R/confint.R lava/R/graph2lvm.R lava/R/dsep.R lava/R/spaghetti.R lava/R/constrain.R lava/R/tr.R lava/R/heavytail.R lava/R/zcolorbar.R lava/R/baptize.R lava/R/partialcor.R lava/R/trim.R lava/R/labels.R lava/R/distribution.R lava/R/fix.R lava/R/ksmooth.R lava/R/lisrel.R lava/R/zgetmplus.R lava/R/sim.lvm.R lava/R/vars.R lava/R/summary.R lava/R/deriv.R lava/R/exogenous.R lava/R/optims.R lava/R/ordreg.R lava/R/transform.R lava/R/parlabels.R lava/R/pcor.R lava/R/missingMLE.R lava/R/merge.R lava/R/stack.R lava/R/lava-package.R lava/R/backdoor.R lava/R/addvar.R lava/R/compare.R lava/R/gof.R lava/R/subgraph.R lava/R/modelsearch.R lava/R/complik.R lava/R/modelPar.R lava/R/model.frame.R lava/R/manifest.R lava/R/vec.R lava/R/fixsome.R lava/R/parameter.R lava/R/measurement.R lava/R/diagtest.R lava/R/measurement.error.R lava/R/information.R lava/R/toformula.R lava/R/correlation.R lava/R/kill.R lava/R/cancel.R lava/R/residuals.R lava/R/gkgamma.R
lava/MD5
lava/DESCRIPTION
lava/man
lava/man/estimate.default.Rd lava/man/addvar.Rd lava/man/vec.Rd lava/man/bmd.Rd lava/man/revdiag.Rd lava/man/eventTime.Rd lava/man/children.Rd lava/man/bootstrap.Rd lava/man/iid.Rd lava/man/path.Rd lava/man/regression-set.Rd lava/man/devcoords.Rd lava/man/Model.Rd lava/man/op_concat.Rd lava/man/predictlvm.Rd lava/man/plot.lvm.Rd lava/man/twindata.Rd lava/man/internal.Rd lava/man/subset.lvm.Rd lava/man/labels-set.Rd lava/man/hubble.Rd lava/man/op_match.Rd lava/man/complik.Rd lava/man/images.Rd lava/man/backdoor.Rd lava/man/serotonin2.Rd lava/man/Combine.Rd lava/man/partialcor.Rd lava/man/makemissing.Rd lava/man/correlation.Rd lava/man/Missing.Rd lava/man/twostage.lvmfit.Rd lava/man/estimate.lvm.Rd lava/man/wrapvec.Rd lava/man/Expand.Rd lava/man/equivalence.Rd lava/man/lava-package.Rd lava/man/toformula.Rd lava/man/confband.Rd lava/man/spaghetti.Rd lava/man/pcor.Rd lava/man/nldata.Rd lava/man/contr.Rd lava/man/vars.Rd lava/man/Col.Rd lava/man/ordreg.Rd lava/man/semdata.Rd lava/man/serotonin.Rd lava/man/missingdata.Rd lava/man/confint.lvmfit.Rd lava/man/fplot.Rd lava/man/parpos.Rd lava/man/zibreg.Rd lava/man/click.Rd lava/man/nsem.Rd lava/man/indoorenv.Rd lava/man/hubble2.Rd lava/man/covariance.Rd lava/man/Graph.Rd lava/man/lava.options.Rd lava/man/intercept.Rd lava/man/diagtest.Rd lava/man/brisa.Rd lava/man/closed.testing.Rd lava/man/compare.Rd lava/man/kill.Rd lava/man/scheffe.Rd lava/man/baptize.Rd lava/man/modelsearch.Rd lava/man/timedep.Rd lava/man/trim.Rd lava/man/calcium.Rd lava/man/commutation.Rd lava/man/cancel.Rd lava/man/bootstrap.lvm.Rd lava/man/lvm.Rd lava/man/dsep.lvm.Rd lava/man/Range.lvm.Rd lava/man/colorbar.Rd lava/man/getSAS.Rd lava/man/density.sim.Rd lava/man/By.Rd lava/man/stack.estimate.Rd lava/man/getMplus.Rd lava/man/tr.Rd lava/man/twostage.Rd lava/man/plotConf.Rd lava/man/bmidata.Rd lava/man/measurement.error.Rd lava/man/org.Rd lava/man/ksmooth2.Rd lava/man/blockdiag.Rd lava/man/multinomial.Rd lava/man/constrain-set.Rd lava/man/sim.Rd lava/man/predict.lvm.Rd lava/man/pdfconvert.Rd lava/man/sim.default.Rd lava/man/gof.Rd lava/man/PD.Rd
lava/INDEX

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