Table 2. .
List of input arguments common to all model functions in the hBayesDM package
| Argument | Required From User | Description |
|---|---|---|
data |
Yes (default = “choose”) | Full path to text file containing data to be used for analysis |
niter |
No (default = 2,000 or higher) | Number of (accepted) samples to be generated by Stan’s HMC sampler |
nwarmup |
No (default = 1,000) | Number of (accepted) samples to be discarded from the beginning of the sampling procedure |
ncore |
No (default = 1) | Number of CPUs to use for parallel computing |
nchain |
No (default = 4) | Number of MCMC chains to run |
nthin |
No (default = 1) | Every nth (accepted) sample from the sampling procedure will be saved. All other samples will be discarded |
inits |
No (default = “random”) | Initial values for the HMC sampler |
indPars |
No (default = “mean”) | How to summarize the parameters upon completion (mean, median, or mode) |
saveDir |
No (default = NULL) | Path to directory where hBayesDM object should be saved upon completion |
| No (default = NULL) | Email address that will be sent a message upon sampling completion | |
modelRegressor |
No (default = FALSE) | Exporting model-based regressors? TRUE or FALSE |
*adapt_delta |
No (default = 0.95) | Acceptance probability of the HMC sampler |
*stepsize |
No (default = 1) | Size of each leapfrog step that the MCMC sampler can take on each new iteration. |
*max_treedepth |
No (default = 10) | Number of leapfrog steps that the MCMC sampler can take on each new iteration. |