A fast engine for computing hierarchical Bayesian model implemented in the Dynamic Model of Choice.
ggdmc implements hierarchical Bayesian, evidence accumulation model (HB-EAM). This release includes drift-diffusion model (Ratcliff, 1978). Based on Voss, Rothermund, and Voss's (2004) fast-dm 30.2 density.c, the DDM in ggdmc implements the equations in their paper as C++ routines plus a new parallel integration function to handle high precision requirement.
ggdmc is derived from Andrew Heathcote's Dynamic Model of Choice (DMC), which has also implemented other numerous EAMs. Identical to DMC, ggdmc uses differential evolution Markov Chain Monte Carlo sampler to search optimal theta and phi that maximise posterior likelihood.
Here is a simple example extracted from Andrew Heathcote's DMC workshop materials. For further details, please see R help pages in this package.
require(ggdmc) ## Use a 6-parameter drift-diffusion model ## The only experimental factor is Stimulus type m1 <- model.dmc( p.map = list(a="1", v="1", z="1", d="1", sz="1", sv="1", t0="1",st0="1"), constants = c(st0=0, d=0), ## Fixed st0 and d at 0 match.map = list(M = list(s1 = "r1", s2 = "r2")), factors = list(S=c("s1", "s2")), ## Two stimulus types responses = c("r1","r2"), ## Two response types type = "rd") ## rd stands for Ratcliff's diffusion ## Set up a prior probability distribution setting p.prior <- prior.p.dmc( dists = rep("tnorm", 6), p1 = c(a=2, v=2.5, z=.5, sz=.3, sv=1, t0=.3), p2 = c(a=.5, v=.5, z=.1, sz=.1, sv=.3, t0=.05), lower = c(0,-5, 0, 0, 0, 0), upper = c(5, 7, 2, 2, 2, 2)) ## Assume a true DDM parameter vector p.vector <- c(a=1, v=1, z=.5, sz=.25, sv=0.2,t0=.15) ## Use simulate function to simulate choice-RT data ## One usually would like to fit his/her own empirical data. dat1 <- simulate(m1, nsim=1e2, p.vector=p.vector) ## Set up a data model instance. This binds the empirical/simulated data with ## the model set-up mdi1 <- data.model.dmc(dat1, m1) ## Initialise a small sample ## (1) iteration number == 250 ## (2) thinning length == 1 ## (3) prior distributions are listed in p.prior ## (4) data == mdi1, an assumed model and a simulated/empirical data frame samples0 <- samples.dmc(nmc=250, p.prior=p.prior, data=mdi1, thin=1) ## Fit the Bayesian model samples0 <- run.dmc(samples0) ## Check if model converged, etc. gelman.diag.dmc(samples0) ## Potential scale reduction factors: ## ## Point est. Upper C.I. ## a 1.16 1.29 ## v 1.20 1.36 ## z 1.18 1.33 ## sz 1.12 1.21 ## sv 1.24 1.48 ## t0 1.16 1.34 plot(samples0) ## Check traceplot to see if chains converged ## Further details and more arguments, please see ?gelman.diag.dmc ?samples.dmc ?run.dmc ?plot.dmc ## For hierarchical Bayesian model ?h.run.dmc ?h.samples.dmc ?plot.dmc.list ?plot.hyper
Successful cases for Windows OS:
Unsuccseeful cases for Windows OS:
From CRAN: install.packages("ggdmc") From source: install.packages("ggdmc_0.1.3.9.tar.gz", repos = NULL, type="source") ### Other supporting packages for DMC (not necessary for ggdmc) install.packages("coda_0.18-1.3.tar.gz", repos = NULL, type="source") install.packages("tnorm_0.1.0.0.tar.gz", repos = NULL, type="source")
If you use this package, please cite the software, for example:
Lin, Y.-S., & Heathcote, A (in preparation). ggdmc: An R package for hierarchical Bayesian evidence accumulation models, using differential evolution Markov Chain Monte Carlo Sampler. Retrieved from https://github.com/TasCL/ggdmc
The ggdmc C++ codes are developed by Yi-Shin Lin.
The R codes mainly are incorporated from DMC developed by Andrew Heathcote].
If there is any bug been introduced inadvertently into DMC R codes, they are probably errors brought in by the first author. Please report any bugs you may find to the first author.
GPL-2. Please see License.md/LICENSE for details.
0.1.3.9 Yi-Shin Lin [email protected]
- Fix more 'overloading ambiguity' errors in tnorm_wrapper.cpp
0.1.3.8 Yi-Shin Lin [email protected]
- Add init.c to register native routines.
0.1.3.7 Yi-Shin Lin [email protected]
- Update to Rcpp 0.12.10 and RcppArmadillo >= 0.7.700.0.0 to resolve 'Rcpp::Nullable' problem.
0.1.3.6 Yi-Shin Lin [email protected]
- Correct 'overloading ambiguity' installation failures on Solaris - Update the link in README.md to canonical url, 'https://CRAN.R-project.org/package=RcppArmadillo'
0.1.3.5 Yi-Shin Lin [email protected]
- First release to the public
0.1.3.4 Yi-Shin Lin [email protected]
- improve ddmc.Rd, dmc.Rd, dprior.Rd. - add dmc.R to generate ggdmc-package.Rd - merge DMC's and ggdmc's plot.prior and rename drawPrior as plot.priors - now ggdmc has its own classes dmc, dmc.list and hyper - ggdmc now uses S3 class to dispatch different summary and plot functions. - Finally, LBA model now is in ggdmc. likelihood.dmc and transform.dmc branch out to e.g., logLik.ddm, logLik.lba_B, becasue two new classes, ddm and lba_B are added. - New modules ggdmc_class.R and ggdmc_eam.R are added. The former defines DMC classes and the latter collects evidence accumulator models. - Add more help pages. - profile.dmc merge with stats's profile - roxygen2 now is also in charge of NAMESPACE
0.1.3.0 Yi-Shin Lin [email protected]
- plot.dmc add function to superimpose prior distribution on top of posterior distribution (ggplot2). - DMC needs to call modified coda to use this function (base).