Update SMC-ABC_Lotka-Volterra_example.ipynb #590
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Added the time array to the plots to correctly represent the independent variable in 2 plots.
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Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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Thanks for the PR. You should also rerun the notebook and then run pre-commit |
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Sorry I am really naive about python and GitHub. I just noticed the error in the notebook when I was adopting the material for use in a math class. I can't even figure outhow to run python on my modified notebook, nor how to download the notebook onto my computer. I just modified the syntax of the plot commands in a way that worked when I did it on a private notebook. I don't expect you to give me a tutorial on pull requests, nor do I want to read a massive amount of documentation. I just wanted to point out a small error in the example notebook which should be very simple to fix for someone who understands the GitHub process better than I do...I'm happy to abandon the issue if it's more bother than it's worth. |
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Wait..one of my students in my class figured out how to overcome the check failure...working on it! |
Run pre-commit and run notebook on changes. Co-authored-by: Dylan Le <[email protected]>
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@OriolAbril reran the notebook and ran pre-commit on changes. |
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View / edit / reply to this conversation on ReviewNB twiecki commented on 2023-11-17T07:57:01Z This doesn't look correct. MacroLens commented on 2023-11-17T16:20:18Z You would be correct. I'm fixing it now, the time scale wasn't applied to the plot on line 6. MacroLens commented on 2023-11-17T16:49:14Z Looks better now. |
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I was flying blind because I didn't see how to actually run the change. Dylan reminded me about cloning (yes, it's been a few years since my last GitHub encounter with some research students, which sent me fleeing). So I'll give it a closer look when I have a bit of time to walk through the mechanics. |
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I added a couple comments. They are on the myst file, but the changes should be made on the notebook, it's pre-commit that syncs the two up again. That should fix the wrong looking plot from the reviewNB comment.
Side note: we are having a docathon starting in 5 minutes (will go on for 3 hours). In case it might be of interest, more info on pymc's discourse
| ax.plot(observed[:, 0], "o", label="prey", c="C0", mec="k") | ||
| ax.plot(observed[:, 1], "o", label="predator", c="C1", mec="k") | ||
| ax.plot(t, observed[:, 0], "o", label="prey", c="C0", mec="k") | ||
| ax.plot(t, observed[:, 1], "o", label="predator", c="C1", mec="k") | ||
| ax.plot(competition_model(None, posterior["a"].mean(), posterior["b"].mean()), linewidth=3) |
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This also needs t as x values
| ax.plot(observed[:, 0], "o", label="prey", c="C0", mec="k") | ||
| ax.plot(observed[:, 1], "o", label="predator", c="C1", mec="k") | ||
| ax.plot(t, observed[:, 0], "o", label="prey", c="C0", mec="k") | ||
| ax.plot(t, observed[:, 1], "o", label="predator", c="C1", mec="k") | ||
| ax.plot(competition_model(None, posterior["a"].mean(), posterior["b"].mean()), linewidth=3) | ||
| for i in np.random.randint(0, size, 75): | ||
| sim = competition_model(None, posterior["a"][i], posterior["b"][i]) |
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and so do the two plot calls right under this line
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Weird I did run the pre-commit. I'll try again.
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Oops I misinterpreted what you meant. I fixed this in f171270.
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You would be correct. I'm fixing it now, the time scale wasn't applied to the plot on line 6. View entire conversation on ReviewNB |
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View / edit / reply to this conversation on ReviewNB MacroLens commented on 2023-11-17T16:48:38Z Should I suppress or correct the warnings? |
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Looks better now. View entire conversation on ReviewNB |
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Thanks! |
* Update SMC-ABC_Lotka-Volterra_example.ipynb Added the time array to the plots to correctly represent the independent variable in 2 plots. * Run pre-commit SMC-ABC_Lotka-Volterra_example (pymc-devs#1) Run pre-commit and run notebook on changes. Co-authored-by: Dylan Le <[email protected]> * fix: add time to the plot command in last plot --------- Co-authored-by: Dylan Le <[email protected]> Co-authored-by: Dylan Le <[email protected]>
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Hi, I have encountered this problem. Do you have any insights on this situation? I would appreciate that you could reply to me. |
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Are other models sampling fine? |
#588 Added the time array to the plots to correctly represent the independent variable in 2 plots
Helpful links
📚 Documentation preview 📚: https://pymc-examples--590.org.readthedocs.build/en/590/