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Add plot_bf #116
Add plot_bf #116
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Sir I had done some changes in multiple files for preventing the ruff errors except init file because they are causing conflicts and these changes do not effect the functionality of the whole codebase. |
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Please, avoid mixing two separate issues in a single PR. Ideally, you should do one to add Bayes_factor and another for fixing ruff or whatever.
src/arviz_plots/plots/bfplot.py
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import logging | |||
from arviz.plots.plot_utils import get_plotting_function |
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You can not use ArviZ. We final goal of the refactoring is that the ArviZ package you are importing will not exist anymore.
The rest of the implementation is not how plots are implemented in Arviz-plots. Please familiarize yourself with the library before adding more changes. See how other plots are implemented, like plot_energy or plot_psense_dist
src/arviz_plots/plots/bfplot.py
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try: | ||
bf, p_at_ref_val = bayes_factor.bayes_factor( | ||
idata, var_name, prior=prior, ref_val=ref_val, return_ref_vals=True | ||
) | ||
except AttributeError as e: | ||
_log.error("Error: %s", e) | ||
raise AttributeError("Bayes factor function not found in arviz.stats.") |
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No need to do this, the function should be available if all packages are properly installed
Also, try to avoid writing very long messages, a lot of text makes it difficult to parse what is useful and what is just blah, blah, blah. Adding information is ok, but try to add only the most relevant information. Adding visuals is a good idea as this is a plotting library. If needed you can add more than one plot, to showcase the effect of different arguments. |
Sir, is it okay that I have added the |
No, you don't need that function. Only use functions from arviz-base, arviz-stats and arviz-plots. The approaches in the old arviz and arviz-plots are completely different, don't try to follow the code in the old one. Instead, think in terms of the elements you need to add. Essentially the minimum elements to get a bayes_factor plot are two distributions and a reference line. Check similar plots like |
@PiyushPanwarFST are you still working on this? |
Sir yes I am working on it and its about to be completed, but I stuck somewhere in dataarray or dataset in bayes_factor |
ok, just checking. |
@aloctavodia I created a new file called bfplot in ArviZ-Plots to add the plotting functionality for Bayes Factor. While calling the bayes_factor function from arviz-stats for computation, I needed to extract the posterior and prior groups, but the prior group is not available in ArviZ-Plots. Even though I loaded the data by adding a new file in inference_diagnostics using load_arviz_data("centered_eight"), the only groups I can see are: Can you please guide me how to solve this issue ? |
Try to write short comments, this could have been "The centered_eight InferenceData does not have a prior group, where I can find an Inference Data with one". Not sure what you are doing but ('/',
'/posterior',
'/posterior_predictive',
'/log_likelihood',
'/sample_stats',
'/prior',
'/prior_predictive',
'/observed_data',
'/constant_data') |
@aloctavodia I have managed to plot the Bayes Factor (BF) for the prior and posterior , but a few tasks are still pending. I wanted to share my progress and get your feedback. ![]() Still figuring out:
3. Noob question: How can I assign different colors for prior and posterior? |
Please add a commit and discuss concrete code |
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pc = azp.plot_bf( | ||
data, | ||
backend="matplotlib", |
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backend="matplotlib", | |
backend="none", |
src/arviz_plots/plots/bfplot.py
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bf_dt = xr.Dataset({var_name: xr.DataArray([0])}) | ||
plot_collection.map( | ||
annotate_xy, | ||
"sd_text", |
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"sd_text", | |
"bf_text", |
![]() Hello @aloctavodia, I have made some updates and let me know if any improvements are needed, thanks |
src/arviz_plots/plots/bfplot.py
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) | ||
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if backend == "matplotlib": ## remove this when we have a better way to handle legends | ||
plot_collection.add_legend("component_group", loc="outside right upper") |
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I don't like the name "component_group" It is here just because I copied it from another plot where that name makes sense. Maybe just group
, or just don't have a title for the legend...
I don't think I will have the time to check this today. So feel free to add more changes if you want, or just wait until tomorrow's feedback. |
I will add documentation and review other aspects as needed. I also agree that the annotations feel a bit clumsy and will work on improving them. I will share the updated version, and you can review it by tomorrow. |
.vscode/settings.json
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{ |
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remove this file
""" | ||
# Bayes_factor | ||
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Plot posterior and prior distributions |
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Plot posterior and prior distributions | |
Compute Bayes factor using Savage–Dickey ratio |
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This needs a rebase
src/arviz_plots/plots/bfplot.py
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plot_collection.map( | ||
annotate_xy, | ||
"bf_text", | ||
text=f"BF10: {bf["BF10"]:.2f}\nBF01: {bf["BF01"]:.2f}", |
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text=f"BF10: {bf["BF10"]:.2f}\nBF01: {bf["BF01"]:.2f}", | |
text=f"BF10: {bf['BF10']:.2f}\nBF01: {bf['BF01']:.2f}", |
improve plot_posterior and add tests for it add minimal docstrings add init to test folder update plot_posterior add some docs add docs and implement some feedback improve api docs ignore mystnb warning add plot_trace (arviz-devs#1) * add trace plot * use convert_to_datatree in tests * fix linters * Add to draft API docs --------- Co-authored-by: Oriol Abril-Pla <[email protected]> rename plot_posterior and small improvements fix test rename source file add style add styles update intro plotcollection update intro plotcollection add ecdf to distplot draft trace_dens draft trace_dens draft Update src/arviz_plots/plots/tracedensplot.py Co-authored-by: Oriol Abril-Pla <[email protected]> Update src/arviz_plots/plots/tracedensplot.py Co-authored-by: Oriol Abril-Pla <[email protected]> Update src/arviz_plots/plots/utils.py Co-authored-by: Oriol Abril-Pla <[email protected]> Update src/arviz_plots/plots/utils.py Co-authored-by: Oriol Abril-Pla <[email protected]> fix missing argument try fixing docs fix docs Issue was due to wrong handling of try except. To avoid depending on matplotlib, it is imported within a try except to register the colormaps and styles, but then it is deleted from the namespace which was happening outside the try except and so arviz_plots failed to import on envs without matplotlib rename dens -> dist update api index Add legend method to PlotCollection and improve docs (arviz-devs#32) * start work on legend and improve docs * add anchor placeholder * work on docs * add backend functions to docs and improve plot_collection docs * add missing files * extend api docs * first attempt at bokeh legend * make no-duplication of backend api docs work * run pre-commit * fix and docs on generate_aes_dt * doc improvements * some doc extensions * improve plot_dist docs * fix bokeh legend generation * add warning to legend method Add plot_forest and tests (arviz-devs#34) * some improvements to PlotCollection * add classmethod tests * add more tests * add divergences to plot_trace * extend tests * add divergence data to test_plots * add plot_forest draft For everything to work, the following features were added to: * support for "__variable__" in aesthetics * default values for common aesthetics * support for dict of datatree input -> multiple models aligned within the same plot * add labels to plot_forest still some backend elements missing for bokeh * further improvements to plot_forest * invert y aes to preserve order top-down * improvements to aes_map defaults and shading * attempt support for InferenceData inputs * plot_dist support for multiple models and docs * update dependencies * add more tests * raise error on wrong use of combined * better support for aesthetics in labels elements Add neutral element concept to aes generation (arviz-devs#35) * First try at neutral element * Fix syntax * Try fixing syntax and improve readability * Fix shade aes default * update and extend tests * update aes_dt to aes_dict conversion * run tests with coverage on CI Fixes and improvements to plot_trace_dist (arviz-devs#36) * very rough draft to fix aesthetic mapping defaults * fix plot_trace_dist and add tests * use neutral element for combined elements * add example to plot_trace Extend and rerun tutorials (arviz-devs#38) * add xlabel to plot_trace * rerun plots_intro notebook * update leftover arviz-base references * write use plotcollection notebook and some improvements * fix scale_fig_size defaults * switch docs theme, default to light version PlotCollection coords attribute for better composability (arviz-devs#39) * prepare reuse of plotting functions * call plot_trace within plot_trace_dist * use plot_dist in plot_trace_dist * add contributing section to docs * fix doc warnings * fix dark-light issue with backend logos * write new_plot docs * improve neutral element behaviour and docs * fix a couple cross-references add none backend and hypothesis tests (arviz-devs#41) * add none backend and hypothesis tests * add more tests with hypothesis and scheduled actions * fix hypothesis yaml syntax * use unset as default for none backend so keys are filtered * add branch reference to issue add codecov token (arviz-devs#42) change action to create issue/comment (arviz-devs#44) fix hypothesis action (arviz-devs#46) * add condition to run if testing failed * try fixing branch name * try adding a more specific link to action logs * switch pytest-store_date command order Prepare initial pre-release (arviz-devs#54) * add links between sub-libraries * bump version * use accessor in plot_forest docstring * bump version and configure publishing Fix issue in plot_dist_trace (arviz-devs#64) don't try to rename artists if they haven't been drawn Adding Ridgeplot to Arviz-Plots (arviz-devs#57) * First commit for adding ridgeplot * Updated `plot_ridge` with 'face' and 'edge' artists now and updated visual elements `line_xy` and `fill_between_y` * Modified density calculation pre-check in plot_ridge and modified visual element functions * Added hypothesis tests for plot_ridge * Added ridge_height as a top level arg and other modifications * final changes --------- Co-authored-by: Oriol (ProDesk) <[email protected]> Removed unused 'extra_data' arg (arviz-devs#73) Add plotly backend and gallery prototype (arviz-devs#61) * plotly backend proof of concept * be more consistend with kwarg handling and defaults * restructure backend dependencies and install process * fix typo in bokeh's remove_ticks * complete plotly backend * gallery prototype * extend docs and tests * add plotly equivalences to glossary * more sensible defaults and kwarg handling * automate gallery generation via sphinx extension * figsize and gallery related fixes * full fledged gallery * remove unused references * update gallery generator * initial plotly support for styles * fix gallery generator processing add pp-obs comparison with plot_forest example (arviz-devs#74) * add pp-obs comparison with plot_forest example * improve example expand style functionality (arviz-devs#75) * expand style functionality * add feedback * Apply suggestions from code review Co-authored-by: Oriol Abril-Pla <[email protected]> --------- Co-authored-by: Oriol Abril-Pla <[email protected]> Improve backend documentation and get plot_forest to follow best practices (arviz-devs#78) * start working on best practices and backend docs * use none backend as documentation base * add images for plotly and none * adapt minigallery directive * use none backend instead of arviz_plots.backend * gallery references and plot sizing improvements * fix typo * pylint * wait until using sphinx 8 * pseudo fix for empty minigallery * modify slightly auto sizing * Apply suggestions from code review Co-authored-by: Osvaldo A Martin <[email protected]> * add see also --------- Co-authored-by: Osvaldo A Martin <[email protected]> Histogram support addition to distplot.py (arviz-devs#47) * WIP histogram addition to distplot.py * Added histogram computing if kind='hist' * reformatted histogram dataarrays into a dataset * Modified histogram dataset plot_axis coords to 'x' and 'y' and added visual element function, backend interface and matplotlib backend function for plotting histogram * Allowing xarray_einstats.histogram() function to determine default number of bins * Modified histogram data restructuring function to include bin edge data and modified docstrings for hist backend interface * added plot_dist test parametrizations for kind=kde, hist, ecdf, adjusted hypothesis time limit to 2 seconds and modified backend hist plotting function * added width to histogram plotting, removed print statements from previous commits and updated restructure_hist_data() docstring * switched histogram computation to arviz stats, modified plot_hist visual element slightly for new returned hist density data structure * added 'density=True' to normalize histogram heights and removed axis by default for histograms * added Bokeh backend for hist visual element and removed ecdf parametrization from test_plot_dist_models * updated docstring, added 'alpha' argument to the 'hist' backend plotting functions, renamed 'plot_hist' to 'hist', modified `remove_axis` logic slightly and set density=True as default in stats_kwargs * Added 'hist' to visuals.rst * deactivate tests for hist kind and multiple models It needs a fix in arviz-stats to work * removed restructure_dist and glyph default artist kwarg in bokeh * updated hist backend interface and matplotlib hist backend function with updates fromrootogram plot * plotly hist and plot_dist improvements --------- Co-authored-by: Oriol Abril-Pla <[email protected]> Add plot_compare (arviz-devs#77) * add plot_compare * directly use plot_backend * add new kwargs * use fill_between_y * docs * remove commented code * use plot_kwargs * use plotcollection * use plotcollection * alow disabling elements * pass pc_kwargs to plotcollection * try to fix example in gallery * add missing import * Update gallery_generator.py * Improve show method for plotcollection * fix 1x1 grid generation in plotly * fix plotly 1x1 plots * add basic test * fix tests * isort * remove redundant array conversion --------- Co-authored-by: Oriol Abril-Pla <[email protected]> rework styles (arviz-devs#88) * rework color palletes * update plotly clean template fix link to github (arviz-devs#91) Add ESS Plot (arviz-devs#58) * First commit for essplot and scatter_xy visual element * update for ess plot and addition of 'x' aesthetic for 'model' dim * addition of quantile plot and updated x aesthetic mapping * Added rugplot to essplot * updates to essplot * fixed default value for arg 'extra_methods' * modified scatter_xy visual element to take into account _process_da_x_y update * Added color/linestyles aesthetics and simplified min_ess plotting * Added annotate_xy visual element, applied to essplot for extra_methods * visual element vertical alignment logic modification and arviz-stats compute_ranks addition attempt * added docs for essplot * tests for essplot * added scatter_xy to visuals.rst * added rug=True to example gallery plot_ess_local * fixes for rugplot issue and hypothesis test failures * shifted mean_ess, sd_ess computing to before plot_kwargs check+artist plotting logic and modified hypothesis tests * Updated plot_ess and tests * updated .toml file for arviz-stats dependency * Modified figsize to more of a plot_forest approach, fixed order of plots in plots.rst and expanded max limit for test methods in testplots.py in .pylintrc * Updated plot_ess docstring * Switched from .grid to .wrap, removed unused figsize coeffs, disabled pylint warning on testplots.py * final fixes now only waiting for us to figure out behaviour and scope in arviz-stats and xarray-einstats * update pyproject requirements * pylint --------- Co-authored-by: Oriol (ProDesk) <[email protected]> fix warning (arviz-devs#99) Adding Plot ESS Evolution (arviz-devs#71) * Initial ess evolution plot updated plot_ess_evolution including a common ess_dataset computing func added mean and sd annotations like essplot docs and example gallery for plot_ess_evolution updated verticalalign logic for mean/sd and correct (although overlaid and not flattened yet) rug is now displayed removed rug plot added tests updated scatter_xy func to plot_ess version fixed docstring altered store_artist for xlabel, ylabel and modified hypothesis tests shifted mean_ess, sd_edd computing to before plot_kwargs check+artist plotting logic updated docstring, added figsizing and set vertical_align for mean and sd text kwargs as setdefault removed 'rankdata' branch of arviz-stats from dependencies docstring typo fix gallery-generator updated for documentation building * remove visual duplicated when rebasing --------- Co-authored-by: Oriol (ProDesk) <[email protected]> Add plot_psense_dist (arviz-devs#93) * Add plot_psense_dist * Update src/arviz_plots/plots/psensedistplot.py Co-authored-by: Oriol Abril-Pla <[email protected]> * Update src/arviz_plots/plots/psensedistplot.py Co-authored-by: Oriol Abril-Pla <[email protected]> * concat da and simplify logic * set sample_dims to sample * refactor * minor fixes and update pyproject to install from GH * support sample_dims argument and all backends * add minigallery to docstring * tweak example * ensure pointinterval only plot does not have yticks * add initial test for psense plot * add test and example * fix test * fix docstring * rename __group__ --------- Co-authored-by: Oriol Abril-Pla <[email protected]> pin datatree and prepare release (arviz-devs#103) * pin datatree and prepare release * update naming for hist_dim to match arviz-stats install arviz-base/stats from github (arviz-devs#104) move out new_ds to arviz-stats (arviz-devs#102) Bump codecov/codecov-action from 4 to 5 (arviz-devs#107) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> update version, dependencies and CI (arviz-devs#110) * update version, dependencies and CI * skip 3.13 until numba release * update rtd env * ignore line too long in gallery template string Use DataTree class from xarray (arviz-devs#111) * start work for xarray datatree compatibility * use datatree from xarray * fix docs * remove unused import Update pyproject.toml (arviz-devs#113) Add energy plot (arviz-devs#108) * add energy plot * remove __variable__, add example * hardcode sampler_dims * use legend only with matplotlib Add plot for distribution of convergence diagnostics (arviz-devs#105) * Add plot for distribution of convergence diagnostics * add ref_line and methods for r-hat * fix docstring * rename, add example * update gallery example * use rhat instead of rhat_rank * update sphinx.configuration key * update sphinx.configuration key * add vline/hline. Co-authored-by: Oriol Abril-Pla <[email protected]> * fix test * fix docstring * fix docstring --------- Co-authored-by: Oriol Abril-Pla <[email protected]> Add separated prior and likelihood groups (arviz-devs#117) * Add separated prior and likelihood groups * upper bound for plotly Add psense_quantities plot (arviz-devs#119) * add psense_quantities plot * remove comment * fix conflicting dimension * update docts * fix color * fix ls * split quantities * fix docstring rename arviz-clean to arviz-variat (arviz-devs#120) rename arviz-clean to arviz-variat add cetrino and vibrant styles to plotly (arviz-devs#121) psense: fix facetting and add xlabel (arviz-devs#123) * fix facetting * add x-label Add summary dictionary arguments (arviz-devs#125) * add summary dictionary arguments * fix spelling plotly: change format of title update in backend (arviz-devs#124) * plotly: change format of title update in backend * update the pyproject.toml file to restrict lower bound of plotly version to 6 Update glossary.md (arviz-devs#126) Add PAV-adjusted calibration plot (arviz-devs#127) * draft pava ppc * add pava-adjusted calibration plot * use dt * fix var name upper bound plotly (arviz-devs#128) use isotonic function that work with datatrees (arviz-devs#131) add reference, fix xlabel (arviz-devs#132) Fix bug when setting some plot_kwargs to false (arviz-devs#134) * fix bug setting when setting some plot_kwargs to false * remove references Add citations (arviz-devs#135) * add citations * reformat citations * fix indentation * fix links * add reference file use <6 version of plotly for documentation and use latest for other purposes (arviz-devs#136) * temporary fix for plotly-plot-rendering-on-webpage * include plotly also in readthedocs fix see algo pava gallery (arviz-devs#137) Add plot_ppc_dist (arviz-devs#138) * add plot_ppc_dist * remove comments * add test and small fixes * fix typo Add warning message for discrete data (arviz-devs#139) * add warning message for discrete data * do not fail on warnings rename plot_pava and minor fixes (arviz-devs#140) fix excesive margins (arviz-devs#141) add arviz-style for bokeh (arviz-devs#122) * add arviz-styles for bokeh * add arviz-styles for bokeh * Update arviz-variat.yml * add more styles Add rootogram (arviz-devs#142) fix examples (arviz-devs#144) Reorganize categories in the gallery (arviz-devs#145) * reorganize categories gallery * update condig * rename remove plots from titles (arviz-devs#146) * remove plots from titles * more renaming * more renaming consistence data_pairs, remove markers pava (arviz-devs#152) added functionality of step histogram for all three backends (arviz-devs#147) * added functionality of step histogram for all three backends * changed user preference format for step histograms * clean * little modifications to make it compatible with cleaned code and to have consistent edgecolor * added test for plot_dist with step value as true * minor fixes: step hist test is not required for 'none' backend --------- Co-authored-by: aloctavodia <[email protected]> use continuous outcome for plot_ppc_dist example (arviz-devs#154) add grid visual (arviz-devs#155) all test cases are passed ruff changes seperating plotting functionality of bayes_factor testing get_plotting funcitonality new implementation of arviz-plot Update bfplot.py it should be something like this. Please, check that it works properly, add docstrings and improve when necessary Improved the plot_bf() function, applied fixes, and added additional assert for test cases Fixed the check for ref_val Added a docstring for plot_bf() Change the backend from matplotlib to none Added a legend to componenet_groups Added few more asserts in test cases Did some other minor fixing and refractoring Signed-off-by: PiyushPanwarFST <[email protected]> Enhance plot_bf() Visualization & Documentation, Fix Linter Issues Adjusted and re-centered BF values for better graph representation. Added plot_bf() function to the documentation. Resolved pylint linter errors in code. Signed-off-by: PiyushPanwarFST <[email protected]> deleting some files and modifying some files
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Hey @aloctavodia, could you please help me reopen this PR ? I am having problems with the rebase. |
On my phone, and I can't. Most likely, because you push changes after closing. I can try later from my laptop. Or maybe you can try to move all changes to a new branch and resubmit |
Add function to plot Bayes Factor approximated as the Savage-Dickey density ratio algorithm
Bayes Factor Plotted graph
ADD figure once you implement the function in arviz_plots, instead of importing it from ArviZ