ggdmc: Dynamic Model of Choice with Parallel Computation, and C++ Capabilities
Version 0.1.3.9

A fast engine for computing hierarchical Bayesian model implemented in the Dynamic Model of Choice.

AuthorYi-Shin Lin [aut, cre], Andrew Heathcote [aut]
Date of publication2017-03-31 10:13:09 UTC
MaintainerYi-Shin Lin <yishin.lin@utas.edu.au>
LicenseGPL-2
Version0.1.3.9
URL https://github.com/TasCL/ggdmc
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ggdmc")

Getting started

README.md

Popular man pages

acf.dmc: Plot an Autocorrelation Matrix
dtnorm: Truncated Normal Distribution
effectiveSize.dmc: Effective Sample Size for Estimating the Mean
fac2df: Convert factor levels to a data frame
gelman.diag.dmc: Gelman and Rubin Convergence Diagnostic
getAccumulatorMatrix: Map a parameter vector to an accumulator matrix
h.run.dmc: Fit an EAM with Multiple Participants
See all...

All man pages Function index File listing

Man pages

acf.dmc: Plot an Autocorrelation Matrix
censor: Censor missing values and RT outliers
data.model.dmc: Bind Data and Models
ddmc: Compute Probability Density of Drift-Diffusion Model
density.dmc: Calculate Probability Density for an Experimental Condition
dprior: Calculate Prior Probability Density for an EAM
Dstats.ddm: Calculate Dstats of DDM Density
dtnorm: Truncated Normal Distribution
effectiveSize.dmc: Effective Sample Size for Estimating the Mean
fac2df: Convert factor levels to a data frame
gelman.diag.dmc: Gelman and Rubin Convergence Diagnostic
getAccumulatorMatrix: Map a parameter vector to an accumulator matrix
get_os: get_os Function
ggdmc: Supersonic DMC
g_minus: Calculate Drift-diffusion Probability Density
h.run.dmc: Fit an EAM with Multiple Participants
h.samples.dmc: Set up a DMC Sample with Multiple Participants
h.simulate.dmc: Simulate Choice-RT Data for Multiple Participants
initialise_data: Set up a DMC Sample for a Participant
initialise_hyper: Set up a DMC Sample for Multiple Participants
likelihood: Calculate Log-Likelihood
mcmc.list.dmc: Create a mcmc.list in DMC format
model.dmc: Creating a Model Object
pairs.dmc: Create a Plot Matrix of Posterior Simulations
p.df.dmc: Gets Parameter Data Frame
phi.as.mcmc.list: Convert Phi to a Theta Vector
pick.stuck.dmc: Find Stuck Chains
plot_cell_density: Plot Distributions for Each Cell
plot_dist: Plot Cell Density
plot.dmc: Plot DMC Samples
plot.dmc.list: Plot a DMC Sample with Multiple Participants
plot.hyper: Plot DMC Samples at the Hyper level
plot.pp.ggdmc: Posterior Predictive Plot
plot_prior: Plot Prior Probability Density
plot_priors: Plot Prior Probability Density
post.predict.ggdmc: Simulate Post-predictive Sample
print_cell_p: Print accumulator x internal parameter type matrix for each...
prior.p.dmc: Makes a list of prior distribution parameters.
profile.dmc: Profile a DMC Object
rprior: Generate Random Numbers from Prior Probability Distribution
run_data: Run a Bayesian EAM Model for Fixed-effect or Random-effect
run.dmc: run function
samples.dmc: Initialising a DMC samples
simulate.dmc: Simulate Responses from an EAM
summary.dmc: Summarise a DMC Sample with One Participant
summary.dmc.list: Summarise a DMC Sample with Multiple Participants
summary.hyper: Summarise a DMC Sample with Multiple Participant at the...
summed_log_likelihood: Sum and Log Probability Density of a EAM model
summed_log_prior: Sum and Log Prior Density of a EAM model
theta.as.mcmc.list: Convert Theta to a mcmc List
transform: Transform Parameter Data Frame
view: Inspect Prior Distribution Settings

Functions

Dstats.ddm Man page Source code
IC.ddm Source code
acf.dmc Man page Source code
add.hyper.dmc Source code
assign.map Source code
assign.pp Source code
assign_pp_pLists Source code
blocked.h.crossover Source code
censor Man page Source code
check.p.vector Source code
checkHyper Source code
checkInputs Source code
checkOutputs Source code
checkTheta Source code
cor.plausible Source code
crossover Source code
crossover.h Source code
data.model.dmc Man page Source code
dbeta_lu Source code
dconstant Source code
ddmc Man page Source code
ddmc_parallel Man page Source code
density.dmc Man page Source code
dgamma_l Source code
dlba.norm Source code
dlba.norm.core Source code
dlnorm_l Source code
dmc Source code
dmc.list Source code
dprior Man page Source code
dtnorm Man page Source code
effectiveSize.dmc Man page Source code
empty.map Source code
fac2df Man page Source code
g_minus Man page Source code
g_minus_parallel Man page Source code
g_plus Man page Source code
g_plus_parallel Man page Source code
gelman.diag.dmc Man page Source code
getAccumulatorMatrix Man page Source code
get_os Man page Source code
ggdmc Man page
ggdmc-package Man page
group_subject_log_likes Source code
group_trial_log_likes Source code
h.log.likelihood.dmc Source code
h.log.posterior.dmc Source code
h.migrate Source code
h.post.predict.dmc Source code
h.profile.dmc Source code
h.run.converge.dmc Source code
h.run.dmc Man page Source code
h.run.unstuck.dmc Source code
h.samples.dmc Man page Source code
h.simulate.dmc Man page Source code
h.summed.log.prior Source code
hyper Source code
initialise_data Man page Source code
initialise_hyper Man page Source code
isMatOrVec Source code
lba_B Source code
likelihood Man page Source code
likelihood.default Man page Source code
likelihood.norm Man page Source code
likelihood.rd Man page Source code
log.likelihood Source code
log.posterior.dmc Source code
log.prior.dmc Source code
loocompare.dmc Source code
looic.dmc Source code
make.hstart Source code
make.level.array Source code
make.r Source code
makePrior.dmc Source code
mcmc.list.dmc Man page Source code
migrate Source code
migrate.h Source code
model.dmc Man page Source code
n1PDFfixedt0.norm Source code
p.df.dmc Man page Source code
p.fun.dmc Source code
pairs.dmc Man page Source code
pd.dmc Source code
phi.as.mcmc.list Man page Source code
pick.stuck.dmc Man page Source code
pick.stucks.dmc Source code
plba.norm Source code
plba.norm.core Source code
pll.dmc Source code
plot.deviance.dmc Source code
plot.dmc Man page Source code
plot.dmc.list Man page Source code
plot.hyper Man page Source code
plot.pp.dmc Source code
plot.pp.ggdmc Man page Source code
plotSpar.dmc Source code
plot_cell_density Man page Source code
plot_dist Man page Source code
plot_prior Man page Source code
plot_priors Man page Source code
post.predict.dmc Source code
post.predict.ggdmc Man page Source code
post_predict_dmc Source code
posterior.lr.dmc Source code
pp.ggdmc Source code
ppl.barplots.dmc Source code
ppp.dmc Source code Source code
print_cell_p Man page Source code
prior.p.dmc Man page Source code
profile.dmc Man page Source code
rbeta_lu Source code
rconstant Source code
rd Source code
rexg Source code
rexgss Source code
rgamma_l Source code
rlba.norm Source code
rlba.norm.gamma Source code
rlba.norm.gammaMR Source code
rlba.norm.lnorm Source code
rlba.normgng Source code
rlnorm_l Source code
rlnr Source code
rlnrgng Source code
rlnrss Source code
rprior Man page Source code
rprior.dmc Source code
rtnorm Man page Source code
run.converge.dmc Source code
run.dmc Man page Source code
run.unstuck.dmc Source code
run_data Man page Source code
run_data_parallel Man page Source code
run_hyper Man page Source code
run_hyper_parallel Man page Source code
samples.dmc Man page Source code
simulate.dmc Man page Source code
summary.dmc Man page Source code
summary.dmc.list Man page Source code
summary.hyper Man page Source code
summed.log.prior Source code
summed_log_likelihood Man page Source code
summed_log_likelihood_parallel Man page Source code
summed_log_prior Man page Source code
theta.as.mcmc.list Man page Source code
transform Man page Source code
transform.norm Man page Source code
transform.rd Man page Source code
trial_log_likes Source code
unstick.dmc Source code
view Man page Source code

Files

inst
inst/examples
inst/examples/ggdmc_4_7_random.R
inst/examples/ggdmc_3_4.R
inst/examples/ggdmc_4_7_fixed.R
inst/include
inst/include/ggdmc
inst/include/ggdmc/ddmc.hpp
inst/include/ggdmc/density.hpp
inst/include/ggdmc/tnorm_wrapper.hpp
inst/include/ggdmc/utility.hpp
inst/include/ggdmc/prior.hpp
inst/include/ggdmc.hpp
src
src/utility.cpp
src/run.cpp
src/Makevars
src/ddmc.cpp
src/tnorm_wrapper.cpp
src/density.cpp
src/prior.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/initialise.cpp
NAMESPACE
NEWS
R
R/dmc_sampling.R
R/dmc_hierarchical.R
R/ggdmc_plotting.R
R/rtdists_extras.R
R/ggdmc_eam.R
R/dmc_model.R
R/ggdmc_class.R
R/RcppExports.R
R/dmc_analysis.R
R/ggdmc_utils.R
R/ggdmc.R
R/dmc_plotting.R
README.md
MD5
DESCRIPTION
man
man/summary.hyper.Rd
man/transform.Rd
man/prior.p.dmc.Rd
man/pick.stuck.dmc.Rd
man/gelman.diag.dmc.Rd
man/density.dmc.Rd
man/simulate.dmc.Rd
man/summary.dmc.list.Rd
man/plot_dist.Rd
man/h.simulate.dmc.Rd
man/phi.as.mcmc.list.Rd
man/plot_prior.Rd
man/fac2df.Rd
man/plot.dmc.list.Rd
man/Dstats.ddm.Rd
man/g_minus.Rd
man/model.dmc.Rd
man/summed_log_prior.Rd
man/ggdmc.Rd
man/likelihood.Rd
man/pairs.dmc.Rd
man/dtnorm.Rd
man/initialise_data.Rd
man/plot.dmc.Rd
man/run_data.Rd
man/acf.dmc.Rd
man/plot_priors.Rd
man/ddmc.Rd
man/plot_cell_density.Rd
man/run.dmc.Rd
man/censor.Rd
man/theta.as.mcmc.list.Rd
man/profile.dmc.Rd
man/h.run.dmc.Rd
man/getAccumulatorMatrix.Rd
man/get_os.Rd
man/plot.pp.ggdmc.Rd
man/print_cell_p.Rd
man/data.model.dmc.Rd
man/summed_log_likelihood.Rd
man/rprior.Rd
man/h.samples.dmc.Rd
man/effectiveSize.dmc.Rd
man/dprior.Rd
man/mcmc.list.dmc.Rd
man/plot.hyper.Rd
man/initialise_hyper.Rd
man/p.df.dmc.Rd
man/summary.dmc.Rd
man/samples.dmc.Rd
man/post.predict.ggdmc.Rd
man/view.Rd
cleanup
ggdmc documentation built on May 19, 2017, 7:26 p.m.

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