Hello, I have a chain saved using the Text backend: db = pm.backends.Text('save1') trace = pm.sample(3000,step=step,start=start,trace=db) I used this to load it within the context of my model: with pm.Model() as model: test=pm.backends.text.load('save1') and it worked, since test is recogni…

I would say only pickling the trace as an intermedia step, and functions operating on the trace should work as intended (e.g., traceplot, sample_ppc etc). But you are right it is indeed better to save the trace as a CSV (for final report or paper), which you can do so by pm.trace_to_dataframe(trace).…

This sounds like a bug, but since there are plans to deprecate text backend maybe you should just pickle the trace instead. [image] Get nan or inf from model.logp (model.test point) is an attestation of incorrectly configured model? Questions Haven’t tried this, but it sho…

I see, thanks. I just read somewhere in the docs that Pickle should not be used for long-term project because the format itself changes often and gets deprecated faster, so I did not chose it. But it’s definitely a better option? Because as for me, a CSV seems pretty simple yet robust…what will pi…

Ah I didn’t know this option, thanks! I’ll try that from now on.

But if you use pm.trace_to_dataframe(trace), and then pickle the dataframe (say), how do you recover the trace from the dataframe in a form from which you can do a traceplot?

I think the best way is to use https://github.com/arviz-devs/arviz We are currently separating the plotting and statistics module from PyMC3 into a general library, potentially for varies python Bayesian packages like pystan, pyro, edward etc (great work mostly done by @aloctavodia and @colcarroll )…

Loaded saved Text Trace does not show any summary or traceplot

Questions

junpenglao October 16, 2017, 2:01pm 2

This sounds like a bug, but since there are plans to deprecate text backend maybe you should just pickle the trace instead.

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Loaded saved Text Trace does not show any summary or traceplot

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