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development version #82

Merged
merged 225 commits into from
Aug 30, 2023
Merged

development version #82

merged 225 commits into from
Aug 30, 2023

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krzyzinskim
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@krzyzinskim krzyzinskim commented Aug 4, 2023 •
edited by mikolajsp
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Before merge:

  • list changes and new functionalities (NEWS.md)
  • make new vignettes and update existing ones
  • update README.md - list all available methods & make roadmap

kapsner and others added 30 commits April 5, 2023 21:28
@kapsner
feat: aggregate survshap across multiple observations
00d6a65
@kapsner
test: added plot for global survshap to unit-test
3bdc619
@mikolajsp
Merge pull request #74 from kapsner/feat-global-survshap
2843273 
Feature: aggregation of SurvSHAP values across multiple observation
@mikolajsp
Add observation_aggregation_method argument to allow for observatio…
c0c779d 
…n wise aggregation using custom functions.
@mikolajsp
Get rid of data.table and make "exact_kernel" shap method work wi…
c6a1f1d 
…th multiple observations
@mikolajsp
Add additional fields in the result object for plotting `aggregated_s…
240d0a8 
…urv_shap`
@mikolajsp
Add plotting of aggregated_surv_shap
e1cfccc
@mikolajsp
Add model_survshap() function and modify survshap to return all cal…
d7887d5 
…culated shaps.
@mikolajsp
Modlify aggregated survshap plotting function.
0015b7f
@mikolajsp
Begin swarmplot
d0f325c
@kapsner
refactor: working on implementation of global survshap
104d087 
- make model_survshap working with new data that was not use to build explainer
- documentation of model_survshap
- minor error handling enhancements
- added unit-tests for global survshap
- removed global survshap tests from test-predict-parts
addresses #75
@kapsner
docs: added working example to model_survshap
72622bf 
and also updated unit-test to allow specifying both, new_observation and N
@kapsner
feat: added n over which shap were aggregated to plot subtitle
3a5aadd
@kapsner
fix: reintroduced missing if-statement for plot title
b8dab05
@krzyzinskim
Merge pull request #77 from kapsner/dev-global-survshap
4c857d1 
Minor enhancements regarding implementation of global survshap
@krzyzinskim
create calculate_integral function as utils
c50c958
@krzyzinskim
remove N from model_survshap
ce3be3b
@krzyzinskim
update aggregation methods in local survshap
8ed8b91
@krzyzinskim
update plots
6ceba5e
@krzyzinskim
update docs
47d7f21
@mikolajsp
Begin integration of additional pdp plots
9b81d48
@krzyzinskim
remove ggbeeswarm from imports
6aff34c
@krzyzinskim
fix using util integration
02e1aab
@krzyzinskim
fix examples
c52f8a3
@krzyzinskim
ggplot with df
5051763
@krzyzinskim
update docs
f0a36b6
@krzyzinskim
make tests faster
9969a92
@krzyzinskim
add ale for numerical variables
f80b8b3
@krzyzinskim
remove old file
a283dde
@krzyzinskim
move error to the right place
e1cce63
krzyzinskim and others added 28 commits August 24, 2023 18:42
@krzyzinskim
fix param name
b89958f
@krzyzinskim
add tests for model_diagnostics
4e7ae04
@krzyzinskim
remove unused arguments
b963d81
@krzyzinskim
fix tests
fe43104
@krzyzinskim
add explainer for flexsurv
91ad9d4
@krzyzinskim
add flexsruv to suggests
eab221f
@krzyzinskim
add simple test for explainer
529624e
@krzyzinskim
fix typo
d0d5a61
@krzyzinskim
add tests
e042a2e
@krzyzinskim
add new times generation method with the median survial time
de8a334
@krzyzinskim
fixes for new times generation method
1eaab03
@krzyzinskim
fix line length in examples
1e81215
@krzyzinskim
fix new times generation method
87cff5d
@krzyzinskim
remove typo
a8d3ab5
@krzyzinskim
improve description of new method
a732489
@krzyzinskim
add model_diagnostics to NEWS.md
26a0506
@krzyzinskim
add new model_survshap plots
2728dbb
@krzyzinskim
add new times generation method to NEWS.md
ff54a7d
@mikolajsp
Add explanations for output_type='chf'
1cda296
@krzyzinskim
fix titles when NULL
38f0b79
@krzyzinskim
fix colors for diagnostic plots
352094e
@mikolajsp
Merge pull request #84 from ModelOriented/dev-2
d9e2af0 
- `model_diagnostics()` for analysis of survival residuals 
- new times generation method for `explain()` - `"survival_quantiles"` that generate times based on survival quantiles from Kaplan-Meier estimator, set as default (!)
- new explainers: for `flexsurv` models and for Python `scikit-survival` models (can be used with `reticulate`)
- new plots for `model_survshap()` - curves (with functional box plot)
- `output_type = "chf"`
@mikolajsp
Fix pkgdown action
6f6f573
@mikolajsp
Fix documentation mismatches
482c3a1
@krzyzinskim
fix plot when there are no outliers
78bcb93
@krzyzinskim
fix profile plots with geom="variable" for categorical variables
eef3583
@krzyzinskim
fix check warnings (context in plots)
e28fb27
@krzyzinskim
bump version
2bc6215
@mikolajsp mikolajsp merged commit f43480c into main Aug 30, 2023
7 checks passed
@mikolajsp mikolajsp deleted the dev-pdp branch September 6, 2023 06:58
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Suggestion on progressr Update vignette
4 participants
@krzyzinskim @mikolajsp @sophhan @kapsner