NEWS.md

In shapviz: SHAP Visualizations

shapviz 0.9.5

User-visible changes

• sv_waterfall() and sv_force(): The x label has been changed from "SHAP value" to "Prediction".

Documentation

• Add vignette for Tidymodels.
• Update vignettes.
• Update README.

shapviz 0.9.4

API improvements

• Support both XGBoost 1.x.x as well as XGBoost 2.x.x, implemented in #144.

Other improvements

• New argument sort_features = TRUE in sv_importance() and sv_interaction(). Set to FALSE to show the features as they appear in your SHAP matrix. In that case, the plots will show the first max_display features, not the most important features. Implements #137.

Bug fixes

• shapviz.xgboost() would fail if a single row is passed. This has been fixed in #142. Thanks @sebsilas for reporting.

shapviz 0.9.3

sv_dependence(): Control over automatic color feature selection

How is the color feature selected, anyway?

If no SHAP interaction values are available, by default, the color feature v' is selected by the heuristic potential_interaction(), which works as follows:

1. If the feature v (the on the x-axis) is numeric, it is binned into nbins bins.
2. Per bin, the SHAP values of v are regressed onto v' and the R-squared is calculated. Rows with missing v' are discarded.
3. The R-squared are averaged over bins, weighted by the number of non-missing v' values.

This measures how much variability in the SHAP values of v is explained by v', after accounting for v.

We have introduced four parameters to control the heuristic. Their defaults are in line with the old behaviour.

• nbin = NULL: Into how many quantile bins should a numeric v be binned? The default NULL equals the smaller of $n/20$ and $\sqrt n$ (rounded up), where $n$ is the sample size.
• color_num Should color features be converted to numeric, even if they are factors/characters? Default is TRUE.
• scale = FALSE: Should R-squared be multiplied with the sample variance of within-bin SHAP values? If TRUE, bins with stronger vertical scatter will get higher weight. The default is FALSE.
• adjusted = FALSE: Should adjusted R-squared be calculated?

If SHAP interaction values are available, these parameters have no effect. In sv_dependence() they are called ih_nbin etc.

This partly implements the ideas in #119 of Roel Verbelen, thanks a lot for your patient explanations!

Further plans?

We will continue to experiment with the defaults, which might change in the future. A good alternative to the current (naive) defaults could be:

• nbins = 7: Smaller than now to not overfit too strongly with factor/character color features.
• color_num = FALSE: To not naively integer encode factors/characters.
• scale = TRUE: To account for non-equal spread in bins.
• adjusted = TRUE: To not put too much weight on factors with many categories.

Other user-visible changes

• sv_dependence(): If color_var = "auto" (default) and no color feature seems to be relevant (SHAP interaction is NULL, or heuristic returns no positive value), there won't be any color scale. Furthermore, in some edge cases, a different color feature might be selected.
• mshapviz() objects can now be rowbinded via rbind() or +. Implemented by @jmaspons in #110.
• mshapviz() is more strict when combining multiple "shapviz" objects. These now need to have identical column names, see #114.

Small changes

• The README is shorter and easier.
• Updated vignettes.
• print.shapviz() now shows top two rows of SHAP matrix.
• Re-activate all unit tests.
• Setting nthread = 1 in all calls to xgb.DMatrix() as suggested by @jmaspons in #109.
• Added "How to contribute" to README.
• permshap() connector is now part of {kerneshap} #122.

Bug fixes

• sv_dependence2D(): In case add_vars are passed, x and/or y are removed from it in order to not use any variable twice. #116.
• split.shapviz() now drops empty levels. They launched an error because empty "shapviz" objects are currently not supported. #117, #118

shapviz 0.9.2

User-visible changes

• sv_importance() of a "mshapviz" object now returns a dodged barplot instead of separate barplots via {patchwork}. Use the new argument bar_type to switch to a stacked barplot (bar_type = "stack"), to "facets" (via {ggplot2}), or "separate" for the old behaviour.

New features

• Added connector to permshap, a package calculating permutation SHAP values for regression and (probabilistic) classification.

Other changes

• Revised vignette on "mshapviz".
• Commenting out most unit tests as they would not pass timings measured on Debian.

shapviz 0.9.1

New features

• dimnames.shapviz() has received a replacement method. You can thus change the column names of SHAP matrix and feature data (as well as SHAP interactions) by colnames(x) <- ..., see https://github.com/ModelOriented/shapviz/issues/98

Maintenance

• Fix for https://github.com/ModelOriented/shapviz/issues/100 (package_version() applied to numeric value will be deprecated in the future)

shapviz 0.9.0

New features

• New plot function sv_dependence2D(): x and y coordinates are two features, while their summed SHAP values are shown on the color scale. If interaction = TRUE, SHAP interaction values are shown on the color scale instead. The function is vectorized in x and/or y. This visualization is especially useful for models with geographic components.
• split(x, f) splits a "shapviz" object x into a "mshapviz" object.

Documentation

• Slight improvements in help/docu.
• New vignette on models with geographic components.
• Added a fantastic house price dataset with about 14,000 houses sold in Miami-Date County, thanks Steven C. Bourassa.

API improvements

• "mshapviz" object created from multioutput "kernelshap" object retains names.

shapviz 0.8.0

API improvement

• For (upcoming) {fastshap} version >0.0.7, fastshap::explain() offers the option shap_only. To conveniently construct the "shapviz" object, use shapviz(fastshap::explain(..., shap_only = FALSE)). This not only passes the SHAP matrix but also the feature data and the baseline. Thanks, Brandon Greenwell!

Documentation

• Better help files
• Switched from "import ggplot2" to "ggplot2::function" code style
• Vignette "Multiple 'shapviz' objects": Fixed mistake in Random Forest + Kernel SHAP example

shapviz 0.7.0

Milestone: Working with multiple 'shapviz' objects

Sometimes, you will find it necessary to work with several "shapviz" objects at the same time:

• To visualize SHAP values of a multiclass or multi-output model.
• To compare SHAP plots of different models.
• To compare SHAP plots between subgroups.

To simplify the workflow, {shapviz} introduces the "mshapviz" object ("m" like "multi"). You can create it in different ways:

• Use shapviz() on multiclass XGBoost or LightGBM models.
• Use shapviz() on "kernelshap" objects created from multiclass/multioutput models.
• Use c(Mod_1 = s1, Mod_2 = s2, ...) on "shapviz" objects s1, s2, ...
• Or mshapviz(list(Mod_1 = s1, Mod_2 = s2, ...))

The sv_*() functions use the {patchwork} package to glue the individual plots together.

See the new vignette for more info and specific examples.

Other new features

• sv_dependence() now allows multiple v and/or color_var to be plotted (glued via {patchwork}).
• {DALEX}: Support for "predict_parts" objects from {DALEX}, thanks to Adrian Stando.
• Aggregated SHAP values: The argument row_id of sv_waterfall() and sv_force() now also allows a vector of integers or a logical vector. If more than one row is selected, SHAP values and predictions are averaged before plotting (aggregated SHAP values in {DALEX}).
• Row bind: "shapviz" objects x1, x2 can now be concatenated in rowwise manner using x1 + x2 or rbind(x1, x2), again thanks to Adrian.
• colnames(): "shapviz" objects x have received a dimnames() function, so you can now, e.g., use colnames(x) to see the feature names.
• Subsetting: "shapviz" x can now be subsetted using x[cond, features].

Maintenance

• We have a new contributor: Adrian Stando - welcome on the SHAP board.
• To be close to my sister package {kernelshap}, I have moved to https://github.com/ModelOriented/shapviz
• Webpage created with "pgkdown"
• New dependency: {patchwork}

Other changes

• Color guides are closer to the plot area. This affects sv_dependence(), sv_importance(kind="bee"), and sv_interaction().
• The lengthy y axis title "SHAP interaction value" in sv_dependence() has been shortened to "SHAP interaction".
• As announced, the argument show_other of sv_importance() has been removed.
• Slightly less picky checks on S_inter.
• print.shapviz() is much more compact, use summary.shapviz() for more info.

Bug fixes

• sv_waterfall(): Using order_fun() would not work as expected with max_display. This has been fixed.
• sv_dependence(): Passing viridis_args = NULL would hide the color guide title. This has been fixed. But please pass viridis_args = list() instead.

shapviz 0.6.0

Change in defaults

• sv_dependence() now uses color_var = "auto" instead of color_var = NULL.
• sv_dependence() now uses "SHAP value" as y label (instead of the more verbose "SHAP value of [feature]").

shapviz 0.5.0

Major improvement: SHAP interaction values

• Introduced API for SHAP interaction values S_inter (3D array):
  • Matrix method: shapviz(object, ..., S_inter = NULL)
  • XGBoost method: shapviz(object, ..., interactions = TRUE)
  • treeshap method: shapviz(object, ...)
• sv_interaction(x) shows matrix of beeswarm plots.
• sv_dependence(x, v = "x1", color_var = "x2", interactions = TRUE) plots SHAP interaction values.
• sv_dependence(x, v = "x1", interactions = TRUE) plots pure main effects of "x1".
• If SHAP interaction values are available, sv_dependence(..., color_var = "auto") uses those to determine the most interacting color variable.
• collapse_shap() also works for SHAP interaction arrays.
• SHAP interaction values can be extracted by get_shap_interactions().

User visible changes

• sv_importance(): In case of too many features, sv_importance() used to collapse the remaining features into an additional bar/beeswarm. This logic has been removed, and the show_other argument has been deprecated.
• By default, sv_dependence() automatically adds horizontal jitter for discrete v. This now also works if v is numeric with at most seven unique values, not only for logicals, factors, and character v.

Compatibility with "ggplot2"

• "ggplot2" 3.4 has replaced the "size" aesthetic in line-based geoms by "linewidth". This has been adapted. "shapviz" now depends on ggplot2 >= 3.4.

Technical changes

• sv_importance() does not use a flipped coordinate system anymore.

shapviz 0.4.1

New functionality

• Hide "other": sv_importance() has received a new argument show_others = TRUE. Set to FALSE to hide the "other" bar/beeswarm.

shapviz 0.4.0

Removed dependencies

The following dependencies have been removed:

• "ggbeeswarm"
• "vipor"
• "beeswarm"

Changes in sv_importance()

• New argument bee_width: Relative width of the beeswarms. The default is 0.4. It replaces the width argument passed via ....
• New argument bee_adjust: Relative adjustment factor of the bandwidth used in estimating the density of the beeswarms. Default is 0.5.
• In case a beeswarm is shown: the ... arguments are now passed to geom_point().

Improvement with Plotly

• plotly::ggplotly() now works for most functionalities of sv_importance(), including beeswarms.

shapviz 0.3.0

Less picky interface

• The argument X of the constructor of shapviz() is now less picky. If it contains columns not present in the SHAP matrix, they are silently dropped. Furthermore, the column order of the SHAP matrix and X is now determined by the SHAP matrix.

Removed (according to depreciation cycle)

• Functions shapviz_from_lgb_predict() and shapviz_from_xgb_predict()
• format_fun argument in sv_force() and sv_waterfall()
• sort_fun argument in sv_waterfall()

Minor changes

• collapse_shap() is not anymore an S3 method. It is just a normal function that can be applied to a matrix.

shapviz 0.2.2

Bug fix

• For R versions < 4.1, sv_importance() would return an error.

Minor improvements

• kernelshap wrapper now also can deal with multioutput models.

shapviz 0.2.1

Major improvements

• Added kernelshap wrapper.

Minor changes

• Removed unnecessary conversion of X_pred from matrix to xgb.DMatrix in shapviz.xgb.Booster().
• Vignette: Added a CatBoost wrapper to the vignette and changed the treeshap() example to a ranger() model.

Maintainance

• Fixed CRAN notes on html5.

shapviz 0.2.0

Major improvements

• Added H2O wrapper.
• Added shapr wrapper.
• Added an optional collapse argument in shapviz(). This is named list specifying which columns in the SHAP matrix are to be collapsed by rowwise summation. A typical application will be to combine the SHAP values of one-hot-encoded dummies and explain them by the corrsponding factor variable.
• Major rework of sv_importance(), see next section.

Major rework of sv_importance()

The calculations behind sv_importance() are unchanged, but defaults and some plot aspects have been reworked.

• Instead of a beeswarm plot, sv_importance() now shows a bar plot by default. Use kind = "beeswarm" to get a beeswarm plot.
• The bar plot of sv_importance() does not show SHAP feature importances as text anymore. Use show_numbers = TRUE to get them back. Furthermore, the numbers are now printed on top of the bars instead on their bottom.
• The new argument show_numbers can be used to to add SHAP feature importance values for all plot types.
• The default of max_display has been increased from 10 to 15.
• The bar width has been reduced from 0.9 to 2/3 relative width. It can be controlled by the new argument bar_width.
• The color bar title of the beeswarm plot can now be manually chosen by the new argument color_bar_title. Set to NULL to remove the color bar altogether.
• The argument format_fun now uses a right-aligned number formatter with aligned decimal separator by default.

Minor changes

• Added dim() method for "shapviz" object, implying nrow() and ncol().
• To allow more flexible formatting, the format_fun argument of sv_waterfall() and sv_force() has been replaced by format_shap to format SHAP values and format_feat to format numeric feature values. By default, they use the new global options "shapviz.format_shap" and "shapviz.format_feat", both with default function(z) prettyNum(z, digits = 3, scientific = FALSE).
• sv_waterfall() now uses the more consistent argument order_fun = function(s) order(abs(s)) instead of the original sort_fun = function(shap) abs(shap) that was then passed to order().
• Added argument viridis_args = getOption("shapviz.viridis_args") to sv_dependence() and sv_importance() to control the viridis color scale options. The default global option equals list(begin = 0.25, end = 0.85, option = "inferno"). For example, to switch to a standard viridis scale, you can either change the default with options(shapviz.viridis_args = NULL) or set viridis_args = NULL.
• Deprecated helper functions shapviz_from_lgb_predict() and shapviz_from_xgb_predict in favour of the collapsing logic (see above). The functions will be removed in version 0.3.0.
• Added 'lightgbm' as "Enhances" dependency.
• Added 'h2o' as "Enhances" dependency.
• Anticipated changes in predict() arguments of LightGBM (data -> newdata, predcontrib = TRUE -> type = "contrib").
• More unit tests.
• Improved documentation.
• Fixed github installation instruction in README and vignette.

shapviz 0.1.0

This is the initial CRAN release.

shapviz documentation built on Sept. 14, 2024, 5:07 p.m.