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

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 publication2016-10-28 10:51:12
MaintainerYi-Shin Lin <yishin.lin@utas.edu.au>
LicenseGPL-2
Version0.1.3.5
https://github.com/TasCL/ggdmc

View on CRAN

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

acf.dmc Man page
censor Man page
data.model.dmc Man page
ddmc Man page
ddmc_parallel Man page
density.dmc Man page
dprior Man page
Dstats.ddm Man page
dtnorm Man page
effectiveSize.dmc Man page
fac2df Man page
gelman.diag.dmc Man page
getAccumulatorMatrix Man page
get_os Man page
ggdmc Man page
ggdmc-package Man page
g_minus Man page
g_minus_parallel Man page
g_plus Man page
g_plus_parallel Man page
h.run.dmc Man page
h.samples.dmc Man page
h.simulate.dmc Man page
initialise_data Man page
initialise_hyper Man page
likelihood Man page
likelihood.default Man page
likelihood.norm Man page
likelihood.rd Man page
mcmc.list.dmc Man page
model.dmc Man page
pairs.dmc Man page
p.df.dmc Man page
phi.as.mcmc.list Man page
pick.stuck.dmc Man page
plot_cell_density Man page
plot_dist Man page
plot.dmc Man page
plot.dmc.list Man page
plot.hyper Man page
plot.pp.ggdmc Man page
plot_prior Man page
plot_priors Man page
post.predict.ggdmc Man page
print_cell_p Man page
prior.p.dmc Man page
profile.dmc Man page
rprior Man page
rtnorm Man page
run_data Man page
run_data_parallel Man page
run.dmc Man page
run_hyper Man page
run_hyper_parallel Man page
samples.dmc Man page
simulate.dmc Man page
summary.dmc Man page
summary.dmc.list Man page
summary.hyper Man page
summed_log_likelihood Man page
summed_log_likelihood_parallel Man page
summed_log_prior Man page
theta.as.mcmc.list Man page
transform Man page
transform.norm Man page
transform.rd Man page
view Man page

Files

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

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