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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 | * 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
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