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

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

Author
Yi-Shin Lin [aut, cre], Andrew Heathcote [aut]
Date of publication
2016-10-28 10:51:12
Maintainer
Yi-Shin Lin <yishin.lin@utas.edu.au>
License
GPL-2
Version
0.1.3.5
URLs

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

Files in this package

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