Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 1] #27
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OriolAbril
reviewed
Feb 4, 2021
Comment on lines
56
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57
| pm.traceplot( | ||
| az.plot_trace( | ||
| trace, varnames=["mu", "r"], lines={"mu": mu_r, "r": corr_r[np.triu_indices(n_var, k=1)]} |
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I am quite sure arviz does not accept varnames, it should be var_names
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Ah, correct! Thanks for that. I updated to arviz 0.11, and got this error
y:212: UserWarning: A valid var_name should be provided, found {'m'} expected from {'mu', 'r'}
warnings.warn(
Traceback (most recent call last):
File "LKJ_correlation.py", line 62, in <module>
run()
File "LKJ_correlation.py", line 56, in run
az.plot_trace(
File "/Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/arviz/plots/traceplot.py", line 238, in plot_trace
axes = plot(**trace_plot_args)
File "/Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/arviz/plots/backends/matplotlib/traceplot.py", line 384, in plot_trace
for _, _, vlines in (j for j in lines if j[0] == var_name and j[1] == selection):
File "/Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/arviz/plots/backends/matplotlib/traceplot.py", line 384, in <genexpr>
for _, _, vlines in (j for j in lines if j[0] == var_name and j[1] == selection):
IndexError: string index out of range
(This error looks related arviz-devs/arviz#988)
Any thoughts why this happened?
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I think I found out why now. It's due to the lines param.
az.plot_trace(
trace, varnames=["mu", "r"], lines={"mu": mu_r, "r": corr_r[np.triu_indices(n_var, k=1)]}
...I removed it to make the az.plot_trac() work.
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Try
lines=(("mu", {}, mu_r), ("r", {}, corr_r[np.triu_indices(n_var, k=1)]))
Yeah @OriolAbril ! I was hoping to get these ~9 PRs merged into the repo, and the proceed into that.
|
OriolAbril
approved these changes
Feb 4, 2021
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Description
The following is a large PR breakdown of PR #16.
Replace PyMC3 dependent plots with arviz plots in case studies & examples.
Replace parameter
sdwithsigma(e.g. some examples havepm.Normal(...sd=...)