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caseyyoungflesh / MCMCvis

R package to visualize, manipulate, and summarize MCMC output
GNU General Public License v3.0
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Function to create text file with model summary #19

Closed caseyyoungflesh closed 3 years ago

caseyyoungflesh commented 5 years ago

MCMCtxt?

Create text file with model summary:

input name of model time elapsed info from MCMCdiag inputs for DELTA, TREE_DEPTH, and STEP_SIZE if Stan obj MCMCsummary (round argument)

caseyyoungflesh commented 5 years ago

Max Rhat min n.eff summary = FALSE argument?

caseyyoungflesh commented 5 years ago

MCMCdiag(object, params = 'all', summary = TRUE, txt = TRUE) outputs diagnostic information can output summary information for params can select params to output if summary = TRUE can write all info to txt file MCMCdiag(fit) --> outputs all diagnostic and summary info to txt file (just time, Rhat, n.eff and summary for JAGS) MCMCdiag(fit, summary = FALSE, txt = FALSE) --> outputs just diagnostic info to terminal

Function should return: time elapsed inputs for adapt delta, max tree depth, initial step size for each chain: num divergences, avg tree depth, step size, mean accept stat, mean energy, number tree exceeds, low BFMI (Y/N) Max Rhat min n.eff MCMCsummary for selected parameters

merge with #18

caseyyoungflesh commented 5 years ago

Possibly create html file with tables for diagnostics?

caseyyoungflesh commented 5 years ago

report_params argument?

caseyyoungflesh commented 3 years ago

arg2 to: 1) create new dir (and put text file there) 2) save out model fit object 3) save data used to fit model

caseyyoungflesh commented 3 years ago

MCMCstats? MCMCdiag?