R: Complete Environment for Bayesian Inference

# Complete Environment for Bayesian Inference

## Documentation for package ‘LaplacesDemon’ version 16.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E G H I J K L M P Q R S T U V W misc

LaplacesDemon-package | Complete Environment for Bayesian Inference

## -- A --

ABB | Approximate Bayesian Bootstrap
AcceptanceRate | Acceptance Rate
as.covar | Proposal Covariance
as.indicator.matrix | Matrix Utility Functions
as.initial.values | Initial Values
as.inverse | Matrix Utility Functions
as.parm.matrix | Matrix Utility Functions
as.parm.names | Parameter Names
as.positive.definite | Matrix Utility Functions
as.positive.semidefinite | Matrix Utility Functions
as.ppc | As Posterior Predictive Check
as.symmetric.matrix | Matrix Utility Functions

## -- B --

BayesFactor | Bayes Factor
BayesianBootstrap | The Bayesian Bootstrap
BayesTheorem | Bayes' Theorem
BigData | Big Data
Blocks | Blocks
BMK.Diagnostic | BMK Convergence Diagnostic
burnin | Burn-in

## -- C --

caterpillar.plot | Caterpillar Plot
CenterScale | Centering and Scaling
cloglog | The log-log and complementary log-log functions
Combine | Combine Demonoid Objects
cond.plot | Conditional Plots
Consort | Consort with Laplace's Demon
Cov2Cor | Matrix Utility Functions
Cov2Prec | Precision
CovEstim | Matrix Utility Functions
CSF | Cumulative Sample Function

## -- D --

dalaplace | Asymmetric Laplace Distribution: Univariate
dallaplace | Asymmetric Log-Laplace Distribution
daml | Asymmetric Multivariate Laplace Distribution
dbern | Bernoulli Distribution
dcat | Categorical Distribution
dcrmrf | Continuous Relaxation of a Markov Random Field Distribution
ddirichlet | Dirichlet Distribution
de.Finetti.Game | de Finetti's Game
deburn | De-Burn
delicit | Prior Elicitation
demonchoice | Demon Choice Data Set
demonfx | Demon FX Data Set
demonsessions | Demon Sessions Data Set
demonsnacks | Demon Snacks Data Set
demontexas | Demon Space-Time Data Set
dgpd | Generalized Pareto Distribution
dgpois | Generalized Poisson Distribution
dhalfcauchy | Half-Cauchy Distribution
dhalfnorm | Half-Normal Distribution
dhalft | Half-t Distribution
dhs | Horseshoe Distribution
dhuangwand | Huang-Wand Distribution
dhuangwandc | Huang-Wand Distribution
dhyperg | Hyperprior-g Prior and Zellner's g-Prior
dinvbeta | Inverse Beta Distribution
dinvchisq | (Scaled) Inverse Chi-Squared Distribution
dinvgamma | Inverse Gamma Distribution
dinvgaussian | Inverse Gaussian Distribution
dinvmatrixgamma | Inverse Matrix Gamma Distribution
dinvwishart | Inverse Wishart Distribution
dinvwishartc | Inverse Wishart Distribution: Cholesky Parameterization
dlaplace | Laplace Distribution: Univariate Symmetric
dlaplacem | Mixture of Laplace Distributions
dlaplacep | Laplace Distribution: Precision Parameterization
dlasso | LASSO Distribution
dllaplace | Log-Laplace Distribution: Univariate Symmetric
dlnormp | Log-Normal Distribution: Precision Parameterization
dmatrixgamma | Matrix Gamma Distribution
dmatrixnorm | Matrix Normal Distribution
dmvc | Multivariate Cauchy Distribution
dmvcc | Multivariate Cauchy Distribution: Cholesky Parameterization
dmvcp | Multivariate Cauchy Distribution: Precision Parameterization
dmvcpc | Multivariate Cauchy Distribution: Precision-Cholesky Parameterization
dmvl | Multivariate Laplace Distribution
dmvlc | Multivariate Laplace Distribution: Cholesky Parameterization
dmvn | Multivariate Normal Distribution
dmvnc | Multivariate Normal Distribution: Cholesky Parameterization
dmvnp | Multivariate Normal Distribution: Precision Parameterization
dmvnpc | Multivariate Normal Distribution: Precision-Cholesky Parameterization
dmvpe | Multivariate Power Exponential Distribution
dmvpec | Multivariate Power Exponential Distribution: Cholesky Parameterization
dmvpolya | Multivariate Polya Distribution
dmvt | Multivariate t Distribution
dmvtc | Multivariate t Distribution: Cholesky Parameterization
dmvtp | Multivariate t Distribution: Precision Parameterization
dmvtpc | Multivariate t Distribution: Precision-Cholesky Parameterization
dnorminvwishart | Normal-Inverse-Wishart Distribution
dnormlaplace | Normal-Laplace Distribution: Univariate Asymmetric
dnormm | Mixture of Normal Distributions
dnormp | Normal Distribution: Precision Parameterization
dnormv | Normal Distribution: Variance Parameterization
dnormwishart | Normal-Wishart Distribution
dpareto | Pareto Distribution
dpe | Power Exponential Distribution: Univariate Symmetric
dsdlaplace | Skew Discrete Laplace Distribution: Univariate
dsiw | Scaled Inverse Wishart Distribution
dslaplace | Skew-Laplace Distribution: Univariate
dst | Student t Distribution: Univariate
dStick | Truncated Stick-Breaking Prior Distribution
dstp | Student t Distribution: Precision Parameterization
dtrunc | Truncated Distributions
dwishart | Wishart Distribution
dwishartc | Wishart Distribution: Cholesky Parameterization
dyangberger | Yang-Berger Distribution
dyangbergerc | Yang-Berger Distribution
dzellner | Hyperprior-g Prior and Zellner's g-Prior

## -- E --

elicit | Prior Elicitation
ESS | Effective Sample Size due to Autocorrelation
extrunc | Truncated Distributions

## -- G --

GaussHermiteCubeRule | Matrix Utility Functions
GaussHermiteQuadRule | Math Utility Functions
Gelfand.Diagnostic | Gelfand's Convergence Diagnostic
Gelman.Diagnostic | Gelman and Rubin's MCMC Convergence Diagnostic
Geweke.Diagnostic | Geweke's Convergence Diagnostic
GIV | Generate Initial Values

## -- H --

Hangartner.Diagnostic | Hangartner's Convergence Diagnostic
Heidelberger.Diagnostic | Heidelberger and Welch's MCMC Convergence Diagnostic
Hermite | Math Utility Functions
Hessian | Matrix Utility Functions

## -- I --

IAT | Integrated Autocorrelation Time
Importance | Variable Importance
interval | Constrain to Interval
invcloglog | The log-log and complementary log-log functions
invlogit | The logit and inverse-logit functions
invloglog | The log-log and complementary log-log functions
is.amodal | The Mode(s) of a Vector
is.appeased | Appeased
is.bayesfactor | Logical Check of Classes
is.bayesian | Logical Check of a Bayesian Model
is.bimodal | The Mode(s) of a Vector
is.blocks | Logical Check of Classes
is.bmk | Logical Check of Classes
is.constant | Logical Check of a Constant
is.constrained | Logical Check of Constraints
is.data | Logical Check of Data
is.demonoid | Logical Check of Classes
is.demonoid.hpc | Logical Check of Classes
is.demonoid.ppc | Logical Check of Classes
is.demonoid.val | Logical Check of Classes
is.hangartner | Logical Check of Classes
is.heidelberger | Logical Check of Classes
is.importance | Logical Check of Classes
is.iterquad | Logical Check of Classes
is.iterquad.ppc | Logical Check of Classes
is.juxtapose | Logical Check of Classes
is.laplace | Logical Check of Classes
is.laplace.ppc | Logical Check of Classes
is.miss | Logical Check of Classes
is.model | Logical Check of a Model
is.multimodal | The Mode(s) of a Vector
is.pmc | Logical Check of Classes
is.pmc.ppc | Logical Check of Classes
is.pmc.val | Logical Check of Classes
is.positive.definite | Matrix Utility Functions
is.positive.semidefinite | Matrix Utility Functions
is.posteriorchecks | Logical Check of Classes
is.proper | Logical Check of Propriety
is.raftery | Logical Check of Classes
is.rejection | Logical Check of Classes
is.sensitivity | Logical Check of Classes
is.square.matrix | Matrix Utility Functions
is.stationary | Logical Check of Stationarity
is.symmetric.matrix | Matrix Utility Functions
is.trimodal | The Mode(s) of a Vector
is.unimodal | The Mode(s) of a Vector
is.vb | Logical Check of Classes
is.vb.ppc | Logical Check of Classes
IterativeQuadrature | Iterative Quadrature

## -- J --

Jacobian | Matrix Utility Functions
joint.density.plot | Joint Density Plot
joint.pr.plot | Joint Probability Region Plot
Juxtapose | Juxtapose MCMC Algorithm Inefficiency

## -- K --

KLD | Kullback-Leibler Divergence (KLD)
KS.Diagnostic | Kolmogorov-Smirnov Convergence Diagnostic

## -- L --

LaplaceApproximation | Laplace Approximation
LaplacesDemon | Laplace's Demon
LaplacesDemon.hpc | Laplace's Demon
LaplacesDemon.RAM | LaplacesDemon RAM Estimate
Levene.Test | Levene's Test
LML | Logarithm of the Marginal Likelihood
logadd | Math Utility Functions
logdet | Matrix Utility Functions
logit | The logit and inverse-logit functions
loglog | The log-log and complementary log-log functions
LossMatrix | Loss Matrix
lower.triangle | Matrix Utility Functions
LPL.interval | Lowest Posterior Loss Interval

## -- M --

MCSE | Monte Carlo Standard Error
MCSS | Monte Carlo Standard Error
MinnesotaPrior | Minnesota Prior
MISS | Multiple Imputation Sequential Sampling
Mode | The Mode(s) of a Vector
Model.Spec.Time | Model Specification Time
Modes | The Mode(s) of a Vector

## -- P --

p.interval | Probability Interval
palaplace | Asymmetric Laplace Distribution: Univariate
pallaplace | Asymmetric Log-Laplace Distribution
partial | Math Utility Functions
pbern | Bernoulli Distribution
phalfcauchy | Half-Cauchy Distribution
phalfnorm | Half-Normal Distribution
phalft | Half-t Distribution
plaplace | Laplace Distribution: Univariate Symmetric
plaplacem | Mixture of Laplace Distributions
plaplacep | Laplace Distribution: Precision Parameterization
pllaplace | Log-Laplace Distribution: Univariate Symmetric
plnormp | Log-Normal Distribution: Precision Parameterization
plot.bmk | Plot Hellinger Distances
plot.demonoid | Plot samples from the output of Laplace's Demon
plot.demonoid.hpc | Plot samples from the output of Laplace's Demon
plot.demonoid.ppc | Plots of Posterior Predictive Checks
plot.importance | Plot Variable Importance
plot.iterquad | Plot the output of 'IterativeQuadrature'
plot.iterquad.ppc | Plots of Posterior Predictive Checks
plot.juxtapose | Plot MCMC Juxtaposition
plot.laplace | Plot the output of 'LaplaceApproximation'
plot.laplace.ppc | Plots of Posterior Predictive Checks
plot.miss | Plot samples from the output of MISS
plot.pmc | Plot samples from the output of PMC
plot.pmc.ppc | Plots of Posterior Predictive Checks
plot.vb | Plot the output of 'VariationalBayes'
plot.vb.ppc | Plots of Posterior Predictive Checks
plotMatrix | Plot a Numerical Matrix
plotSamples | Plot Samples
PMC | Population Monte Carlo
PMC.RAM | PMC RAM Estimate
pnormm | Mixture of Normal Distributions
pnormp | Normal Distribution: Precision Parameterization
pnormv | Normal Distribution: Variance Parameterization
PosteriorChecks | Posterior Checks
ppareto | Pareto Distribution
ppe | Power Exponential Distribution: Univariate Symmetric
Prec2Cov | Precision
prec2sd | Precision
prec2var | Precision
predict.demonoid | Posterior Predictive Checks
predict.iterquad | Posterior Predictive Checks
predict.laplace | Posterior Predictive Checks
predict.pmc | Posterior Predictive Checks
predict.vb | Posterior Predictive Checks
print.demonoid | Print an object of class 'demonoid' to the screen.
print.heidelberger | Print an object of class 'heidelberger' to the screen.
print.iterquad | Print an object of class 'iterquad' to the screen.
print.laplace | Print an object of class 'laplace' to the screen.
print.miss | Print an object of class 'miss' to the screen.
print.pmc | Print an object of class 'pmc' to the screen.
print.raftery | Print an object of class 'raftery' to the screen.
print.vb | Print an object of class 'vb' to the screen.
psdlaplace | Skew Discrete Laplace Distribution: Univariate
pslaplace | Skew-Laplace Distribution: Univariate
pst | Student t Distribution: Univariate
pstp | Student t Distribution: Precision Parameterization
ptrunc | Truncated Distributions

## -- Q --

qalaplace | Asymmetric Laplace Distribution: Univariate
qallaplace | Asymmetric Log-Laplace Distribution
qbern | Bernoulli Distribution
qcat | Categorical Distribution
qhalfcauchy | Half-Cauchy Distribution
qhalfnorm | Half-Normal Distribution
qhalft | Half-t Distribution
qlaplace | Laplace Distribution: Univariate Symmetric
qlaplacep | Laplace Distribution: Precision Parameterization
qllaplace | Log-Laplace Distribution: Univariate Symmetric
qlnormp | Log-Normal Distribution: Precision Parameterization
qnormp | Normal Distribution: Precision Parameterization
qnormv | Normal Distribution: Variance Parameterization
qpareto | Pareto Distribution
qpe | Power Exponential Distribution: Univariate Symmetric
qsdlaplace | Skew Discrete Laplace Distribution: Univariate
qslaplace | Skew-Laplace Distribution: Univariate
qst | Student t Distribution: Univariate
qstp | Student t Distribution: Precision Parameterization
qtrunc | Truncated Distributions

## -- R --

Raftery.Diagnostic | Raftery and Lewis's diagnostic
ralaplace | Asymmetric Laplace Distribution: Univariate
rallaplace | Asymmetric Log-Laplace Distribution
raml | Asymmetric Multivariate Laplace Distribution
rbern | Bernoulli Distribution
rcat | Categorical Distribution
rcrmrf | Continuous Relaxation of a Markov Random Field Distribution
rdirichlet | Dirichlet Distribution
read.matrix | Matrix Utility Functions
RejectionSampling | Rejection Sampling
rgpd | Generalized Pareto Distribution
rhalfcauchy | Half-Cauchy Distribution
rhalfnorm | Half-Normal Distribution
rhalft | Half-t Distribution
rhs | Horseshoe Distribution
rhuangwand | Huang-Wand Distribution
rhuangwandc | Huang-Wand Distribution
rinvbeta | Inverse Beta Distribution
rinvchisq | (Scaled) Inverse Chi-Squared Distribution
rinvgamma | Inverse Gamma Distribution
rinvgaussian | Inverse Gaussian Distribution
rinvwishart | Inverse Wishart Distribution
rinvwishartc | Inverse Wishart Distribution: Cholesky Parameterization
rlaplace | Laplace Distribution: Univariate Symmetric
rlaplacem | Mixture of Laplace Distributions
rlaplacep | Laplace Distribution: Precision Parameterization
rlasso | LASSO Distribution
rllaplace | Log-Laplace Distribution: Univariate Symmetric
rlnormp | Log-Normal Distribution: Precision Parameterization
rmatrixnorm | Matrix Normal Distribution
rmvc | Multivariate Cauchy Distribution
rmvcc | Multivariate Cauchy Distribution: Cholesky Parameterization
rmvcp | Multivariate Cauchy Distribution: Precision Parameterization
rmvcpc | Multivariate Cauchy Distribution: Precision-Cholesky Parameterization
rmvl | Multivariate Laplace Distribution
rmvlc | Multivariate Laplace Distribution: Cholesky Parameterization
rmvn | Multivariate Normal Distribution
rmvnc | Multivariate Normal Distribution: Cholesky Parameterization
rmvnp | Multivariate Normal Distribution: Precision Parameterization
rmvnpc | Multivariate Normal Distribution: Precision-Cholesky Parameterization
rmvpe | Multivariate Power Exponential Distribution
rmvpec | Multivariate Power Exponential Distribution: Cholesky Parameterization
rmvpolya | Multivariate Polya Distribution
rmvt | Multivariate t Distribution
rmvtc | Multivariate t Distribution: Cholesky Parameterization
rmvtp | Multivariate t Distribution: Precision Parameterization
rmvtpc | Multivariate t Distribution: Precision-Cholesky Parameterization
rnorminvwishart | Normal-Inverse-Wishart Distribution
rnormlaplace | Normal-Laplace Distribution: Univariate Asymmetric
rnormm | Mixture of Normal Distributions
rnormp | Normal Distribution: Precision Parameterization
rnormv | Normal Distribution: Variance Parameterization
rnormwishart | Normal-Wishart Distribution
rpareto | Pareto Distribution
rpe | Power Exponential Distribution: Univariate Symmetric
rsdlaplace | Skew Discrete Laplace Distribution: Univariate
rsiw | Scaled Inverse Wishart Distribution
rslaplace | Skew-Laplace Distribution: Univariate
rst | Student t Distribution: Univariate
rStick | Truncated Stick-Breaking Prior Distribution
rstp | Student t Distribution: Precision Parameterization
rtrunc | Truncated Distributions
rwishart | Wishart Distribution
rwishartc | Wishart Distribution: Cholesky Parameterization
rzellner | Hyperprior-g Prior and Zellner's g-Prior

## -- S --

sd2prec | Precision
sd2var | Precision
SensitivityAnalysis | Sensitivity Analysis
server_Listening | Server Listening
SIR | Sampling Importance Resampling
SparseGrid | Matrix Utility Functions
Stick | Truncated Stick-Breaking
summary.demonoid.ppc | Posterior Predictive Check Summary
summary.iterquad.ppc | Posterior Predictive Check Summary
summary.laplace.ppc | Posterior Predictive Check Summary
summary.miss | MISS Summary
summary.pmc.ppc | Posterior Predictive Check Summary
summary.vb.ppc | Posterior Predictive Check Summary

## -- T --

Thin | Thin
tr | Matrix Utility Functions
TransitionMatrix | Matrix Utility Functions

## -- U --

upper.triangle | Matrix Utility Functions

## -- V --

Validate | Holdout Validation
var2prec | Precision
var2sd | Precision
VariationalBayes | Variational Bayes
vartrunc | Truncated Distributions

## -- W --

WAIC | Widely Applicable Information Criterion

## -- misc --

.colVars | Complete Environment for Bayesian Inference
.iqagh | Complete Environment for Bayesian Inference
.iqaghsg | Complete Environment for Bayesian Inference
.iqcagh | Complete Environment for Bayesian Inference
.laaga | Complete Environment for Bayesian Inference
.labfgs | Complete Environment for Bayesian Inference
.labhhh | Complete Environment for Bayesian Inference
.lacg | Complete Environment for Bayesian Inference
.ladfp | Complete Environment for Bayesian Inference
.lahar | Complete Environment for Bayesian Inference
.lahj | Complete Environment for Bayesian Inference
.lalbfgs | Complete Environment for Bayesian Inference
.lalm | Complete Environment for Bayesian Inference
.lanm | Complete Environment for Bayesian Inference
.lanr | Complete Environment for Bayesian Inference
.lapso | Complete Environment for Bayesian Inference
.larprop | Complete Environment for Bayesian Inference
.lasgd | Complete Environment for Bayesian Inference
.lasoma | Complete Environment for Bayesian Inference
.laspg | Complete Environment for Bayesian Inference
.lasr1 | Complete Environment for Bayesian Inference
.latr | Complete Environment for Bayesian Inference
.mcmcadmg | Complete Environment for Bayesian Inference
.mcmcafss | Complete Environment for Bayesian Inference
.mcmcagg | Complete Environment for Bayesian Inference
.mcmcahmc | Complete Environment for Bayesian Inference
.mcmcaies | Complete Environment for Bayesian Inference
.mcmcam | Complete Environment for Bayesian Inference
.mcmcamm | Complete Environment for Bayesian Inference
.mcmcamm.b | Complete Environment for Bayesian Inference
.mcmcamwg | Complete Environment for Bayesian Inference
.mcmccharm | Complete Environment for Bayesian Inference
.mcmcdemc | Complete Environment for Bayesian Inference
.mcmcdram | Complete Environment for Bayesian Inference
.mcmcdrm | Complete Environment for Bayesian Inference
.mcmcess | Complete Environment for Bayesian Inference
.mcmcgg | Complete Environment for Bayesian Inference
.mcmcggcp | Complete Environment for Bayesian Inference
.mcmcggcpp | Complete Environment for Bayesian Inference
.mcmcggdp | Complete Environment for Bayesian Inference
.mcmcggdpp | Complete Environment for Bayesian Inference
.mcmcgibbs | Complete Environment for Bayesian Inference
.mcmcharm | Complete Environment for Bayesian Inference
.mcmchmc | Complete Environment for Bayesian Inference
.mcmchmcda | Complete Environment for Bayesian Inference
.mcmcim | Complete Environment for Bayesian Inference
.mcmcinca | Complete Environment for Bayesian Inference
.mcmcmala | Complete Environment for Bayesian Inference
.mcmcmcmcmc | Complete Environment for Bayesian Inference
.mcmcmtm | Complete Environment for Bayesian Inference
.mcmcmwg | Complete Environment for Bayesian Inference
.mcmcnuts | Complete Environment for Bayesian Inference
.mcmcohss | Complete Environment for Bayesian Inference
.mcmcram | Complete Environment for Bayesian Inference
.mcmcrdmh | Complete Environment for Bayesian Inference
.mcmcrefractive | Complete Environment for Bayesian Inference
.mcmcrj | Complete Environment for Bayesian Inference
.mcmcrss | Complete Environment for Bayesian Inference
.mcmcrwm | Complete Environment for Bayesian Inference
.mcmcsamwg | Complete Environment for Bayesian Inference
.mcmcsgld | Complete Environment for Bayesian Inference
.mcmcslice | Complete Environment for Bayesian Inference
.mcmcsmwg | Complete Environment for Bayesian Inference
.mcmcthmc | Complete Environment for Bayesian Inference
.mcmctwalk | Complete Environment for Bayesian Inference
.mcmcuess | Complete Environment for Bayesian Inference
.mcmcusamwg | Complete Environment for Bayesian Inference
.mcmcusmwg | Complete Environment for Bayesian Inference
.rowVars | Complete Environment for Bayesian Inference
.vbsalimans2 | Complete Environment for Bayesian Inference