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Update the imports #377

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wants to merge 183 commits into from
Closed

Update the imports #377

wants to merge 183 commits into from

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LHBO
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@LHBO LHBO commented Feb 19, 2024

In this pull request, we remove imports that are no longer needed in the shapr-package.R file. These imports were important at an earlier version of the shapr package, but were not removed when the corresponding dependencies were removed.

@LHBO
Add torch modules
87dc45d
@LHBO
Add vaeac method
a62e3c1
@LHBO
Vignettes
5976911
@LHBO
VAEAC tests
7683954
@LHBO
Plot tests
d9660ee
@LHBO
vaeac setup tests
1c495cd
@LHBO
Add vaeac to explain
cf64c85
@LHBO
Add vaeac to explain_forecast
4c4b128
@LHBO
Added plot function that plots several explanations at the same time
673d182
@LHBO
Added missing data.table:: in plot function
8fef07e
@LHBO
Refactored plot_SV_several_approaches
a5b9b04
@LHBO
Fixed vignette where $MSEv_bar was no longer needed.
8abd92a
@LHBO
stylr
c1db340
@LHBO
Fixed such that can plot explanations even when using different combi…
63e659d 
…nations
@LHBO
Updated references
0c29399
@LHBO
Added example file to show how to use plot_SV_several_approaches()
26cf176
@LHBO
Updated examples
ea62fca
@LHBO
Added tests
e6aa28d
@LHBO
skip_connection_masked_enc_dec
0d148f8
@LHBO
mask_gen_these_coalitions_prob
5d66600
@LHBO
mask_gen_these_coalitions
41796f0
@LHBO
extra_params_skip_con_mask_enc
5a4fe94
@LHBO
num_train_param
54a5fc6
@LHBO
stylr
30f1921
@LHBO
vaeac.num_different_vaeac_initiate
e404b22
@LHBO
transform_all_cont_features
47ffc46
@LHBO
exp_trans_cont_features_func
7917b56
@LHBO
categorical_parse_params_col
a777f58
@LHBO
GaussCatSamplerMostLikely
65977bb
@LHBO
GaussCat
7e79e14
martinju and others added 23 commits February 16, 2024 08:59
@martinju
actually run the chunks in the vignettes
10fb862
@martinju
vignette figures + more name fixing
68fb88d
@martinju
gitignore vignette cache. Will do it manually locally anyway
25db7b3
@martinju
more vignette file updates
cd0df49
@martinju
put the original vignette into the long-vignette format as well
5d28b8a 
for speed-up + such that pkgdown don't need the torch stuff
@martinju
fix typo making tests on GHA fail
4a3b4aa
@martinju
forgot to update rds files
7e5bec3
@LHBO
Added main vignette to the .Rbuildignore file too
70a3048
@LHBO
Added vignettes figure and cache map to buildignore
b7a85b3
@LHBO
Updated what to remove from shapr object when not saving vaeac model.…
4060144 
… This is to reduce the .rds save files size and to remove time dependent random path names
@LHBO
Updated questions before publising on cran
93311fa
@LHBO
Updated snapshots for vaeac test functions
b61ac8f
@LHBO
Set separate figure and cache paths for the vignettes
96e87a0
@LHBO
Updated broken links in vaeac vignette
4ce7e98
@LHBO
Updated the figure parameters
31baa9c
@LHBO
Run the vignettes and deleted old files
6be1ee0
@LHBO
stylr
e4e1b58
@LHBO
Put all stats imports on one line
f5f0d69
@LHBO
Removed model.frame
48ed1bb
@LHBO
removed rect
922edc0
@LHBO
Updating rbuildignore
c5a1e5c
@LHBO
Figuring out what imports to remove
034dea2
@LHBO
Get the same check results as before removing imports, so everything …
6b0237d 
…should work.
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LHBO commented Feb 19, 2024

Note that several more can be removed if one use e.g. data.table::copy instead of just copy. Currently there is no consistency across methods when to include the library prefix and not. Discuss with Martin.

Also, sourceCpp is no longer needed, but removing that makes the checks give a lot of warnings.

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LHBO commented Feb 27, 2024

Should remove whitespace around the number of features.

Error in check_approach(internal) : approach must be one of the following: categorical, copula, ctree, empirical, gaussian, independence, regression_separate, timeseries, vaeac or a vector of length one less than the number of features ( 3 ), with only the above strings.

@martinju martinju closed this Apr 16, 2024
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Do this in #391

@LHBO LHBO mentioned this pull request Apr 16, 2024
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@LHBO LHBO deleted the Lars/shapr_cleanup branch April 18, 2024 08:04
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@LHBO @martinju