`slopes` documentation #701

GStechschulte · 2023-08-01T04:58:39Z

This PR provides documentation for PR #699 (slopes and plot_slopes). The notebook provides the following sections:

interpretation of regression coefficients under three scenarios and how this can be difficult and cumbersome: (1) gaussian model with no link function, (2) gaussian model with interactions, and (3) GLMs
how average predictive slopes are computed
how to use slopes and plot_slopes, and the benefits under the following:
- user provided values (single and multiple)
- conditional slopes (using a GLM with interaction terms)
- unit-level slopes
- average slopes
- average by subgroup slopes
- interpreting coefficients as an elasticity (or semi-elasticity)
- slopes of categorical covariates

…uilding summary dataframe

…d comparisons

…mproved parsing of uncertainty dict

…ple values

…e values to other methods

…ing when len(wrt) > 2

…the data

merge slopes branch

review-notebook-app · 2023-08-01T04:58:43Z

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codecov-commenter · 2023-08-01T06:11:14Z

Codecov Report

Merging #701 (8a4226a) into main (457eee3) will increase coverage by 0.16%.
The diff coverage is 91.81%.

❗ Current head 8a4226a differs from pull request most recent head 8847ad3. Consider uploading reports for the commit 8847ad3 to get more accurate results

@@            Coverage Diff             @@
##             main     #701      +/-   ##
==========================================
+ Coverage   89.57%   89.73%   +0.16%     
==========================================
  Files          43       43              
  Lines        3522     3499      -23     
==========================================
- Hits         3155     3140      -15     
+ Misses        367      359       -8

Files Changed	Coverage Δ
bambi/plots/plotting.py	`85.24% <88.88%> (+0.28%)`	⬆️
bambi/plots/effects.py	`90.94% <90.75%> (+1.69%)`	⬆️
bambi/plots/utils.py	`86.82% <92.98%> (+0.06%)`	⬆️
bambi/plots/__init__.py	`100.00% <100.00%> (ø)`
bambi/plots/create_data.py	`100.00% <100.00%> (ø)`
bambi/plots/plot_types.py	`73.39% <100.00%> (ø)`

... and 1 file with indirect coverage changes

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docs/notebooks/plot_slopes.ipynb

tomicapretto · 2023-08-03T01:15:48Z

excellent work @GStechschulte. Just left some comments. I don't think further additions are needed, only some removals and maybe simplifications. Thanks a lot!

GStechschulte · 2023-08-03T15:33:19Z

excellent work @GStechschulte. Just left some comments. I don't think further additions are needed, only some removals and maybe simplifications. Thanks a lot!

Thanks @tomicapretto , and also for the review!

docs/notebooks/plot_slopes.ipynb

aloctavodia · 2023-08-03T17:54:24Z

docs/notebooks/plot_slopes.ipynb

@@ -0,0 +1,2503 @@
+{


instead of having to do two imports we should just import bambi as bmb and then call

bmb.slopes, bmb.plot_slopes, etc

Reply via ReviewNB

I will change this in PR #699 and then merge into this branch 👍🏼

docs/notebooks/plot_slopes.ipynb

aloctavodia · 2023-08-03T17:54:43Z

This is fantastic!

GStechschulte · 2023-08-05T05:31:28Z

This is fantastic!

Thank you @aloctavodia! And thanks for the feedback. Much appreciated :)

…iew.

tomicapretto · 2023-08-09T13:51:57Z

@GStechschulte there are some conflicts now 😅

@aloctavodia if you don't have any further comments i will merge once the conflicts are resolved

GStechschulte · 2023-08-10T20:06:04Z

@GStechschulte there are some conflicts now 😅

@aloctavodia if you don't have any further comments i will merge once the conflicts are resolved

Good to go now 😄

GStechschulte added 30 commits July 22, 2023 10:27

add slopes and plot_slopes

b125a47

common create data function for comparisons and slopes

bb4ec6a

add slopes and PredictiveDifference class for computing effects and b…

da1b6d4

…uilding summary dataframe

Assign colors for single covariates by @tjburch

c7f6410

add plot_slopes and common plotting function for slopes and comparisons

689641a

common VariableInfo class and default value computation for slopes an…

6935ceb

…d comparisons

reorder imports alphabetically

8bd459c

improved docstring for plot_slopes

ff60f08

move private inner functions outside of 'create_differences_data' func

4a4482b

slopes supports multiple values, added args. to 'get_estimate', and i…

dd8bd43

…mproved parsing of uncertainty dict

add color='C0' to fix color bug

dbb7cc1

update to VariableInfo class to allow slopes with user provided multi…

e326a6f

…ple values

add support for semi-elasticities, move slopes and setting of variabl…

392625f

…e values to other methods

update ValueError to include semi-elasticities

a8f72b3

raise ValueError is slopes not in semi-elasticities

d76e3e1

run black code formatting

b883df6

slopes and plot_slopes docs

bc86e4b

if slopes effect, convert columns that are not 'wrt' to original dtype

c04858e

pass transforms as arg. to PredictiveDifferences

eebfb34

raise ValueError if user attempts to use 'plot_slopes' without averag…

9a541ac

…ing when len(wrt) > 2

fix set_default_values bug for 'comparisons' by applying the mean to …

43e9ead

…the data

add 'plot_slopes' tests

1d8888d

docstring fixes / enhancements

dc77947

Merge remote-tracking branch 'origin/slopes' into slopes-docs

df977c8

merge slopes branch

plot_slopes docs outline

294c3d7

introduction, interpreting slopes, and computing slopes

1f41c13

well switching example from Regression and Other Stories

93409ed

add all quantities of interest and elasticities section

2d6135c

bug fix when computing > 3 variable values of interest

4e1461e

slopes of categorical values

6613958

GStechschulte added 2 commits August 1, 2023 06:34

delete commented code

99c84be

review notebook for grammer, etc.

4c3072d

GStechschulte added 2 commits August 1, 2023 07:00

change >= 2 to > 2 for when arg. is needed for

4f89751

run black formatting

67a41d7

add epsilon to regression equation

f69523a

tomicapretto reviewed Aug 3, 2023

View reviewed changes

aloctavodia reviewed Aug 3, 2023

View reviewed changes

GStechschulte added 2 commits August 6, 2023 14:40

delete, edits, and additions to notebook commentary based on code rev…

02ddbcd

…iew.

changes u, v to w, c

8a4226a

GStechschulte requested review from tomicapretto and aloctavodia August 6, 2023 12:41

tomicapretto approved these changes Aug 7, 2023

View reviewed changes

GStechschulte added 2 commits August 10, 2023 16:43

Merge 'upstream/main' into slopes-docs

8847ad3

resolve pylint error by disabling error

035a90a

tomicapretto merged commit fcf8ab5 into bambinos:main Aug 10, 2023
4 checks passed

GStechschulte deleted the slopes-docs branch January 21, 2024 20:19

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`slopes` documentation #701

`slopes` documentation #701

GStechschulte commented Aug 1, 2023

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codecov-commenter commented Aug 1, 2023 •

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tomicapretto commented Aug 9, 2023

GStechschulte commented Aug 10, 2023

slopes documentation #701

slopes documentation #701

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`slopes` documentation #701

`slopes` documentation #701

codecov-commenter commented Aug 1, 2023 •

edited

GStechschulte commented Aug 3, 2023 •

edited

aloctavodia Aug 3, 2023 •

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GStechschulte commented Aug 5, 2023 •

edited