Code

Lars/add MSEv eval criterion#357

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LHBO merged 165 commits intoNorskRegnesentral:masterNorskRegnesentral/shapr:masterfrom LHBO:Lars/add_MSEv_eval_criterionLHBO/shapr:Lars/add_MSEv_eval_criterionCopy head branch name to clipboardDec 11, 2023

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Commits on Aug 24, 2023

• Bugfix in prepare_data() related to vector of approaches. When using several approaches the old version only used the first approach. Verified this by adding a print in each prepare_data.approach…

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• Implemented function that computes the MSEv evaluation criterion for all approaches as long as internal$parameters$output_size == 1.

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• Plot the MSEv evaluation criterion.

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• Added a section about the MSEv criterion in the vignette. This is s adraft and might need some polishing.

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• # Lars have added n_combinations - 1 as a possibility, as the function check_n_batches threw an error for the vignette with gaussian approach with n_combinations = 8 and n_batches = NULL, a…

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• Samll typo.

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• Fixed bug. All messages says "n_combinations is larger than or equal to 2^m", but all the test only tested for "larger than". I.e., if the user specified n_combinations = 2^m in the call to shapr::…

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Commits on Aug 30, 2023

• Changed to exclude the coalitions which are not effected by the approach by default.

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• Added example to the roxygen. This is technically not needed as it is an internal function.

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• Added some parameters to the plot function to make it more flexiable and to make it easier for the user to controll what figures that are made

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• Updated code as I had only changed the legend for the fill (which works with bars), but not the col (which works for lines/points).

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• Added the updated namespace file. Maybe that is why the tests on github did not work beforehand.

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Commits on Aug 31, 2023

• Added script demonstrating the bug that shapr does not enter the exact mode when n_combinations = 2^m, before the bugfix.

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• Added (tentative) test that checks that shapr enters exact mode when n_combinations >= 2^m. Remove the large comment after discussing that with Martin.

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• Added script that demonstrates the bug before the bugfix, and added test checking that we do not get an error when runing the code after the bugfix has been applied.

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• Fixed lint warnings in approach.R.

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Commits on Sep 1, 2023

• Added ctree in the example in roxygen

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• Add manuals for the two funtions realted to MSEv criterion.

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• Updated plot function (fixed some inconsistencies) and added detailed examples. Plan to make tests out of them.

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• Started to make tests, but ran into a shapr bug.

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Commits on Sep 4, 2023

• Added two parameters to the internal$parameters list which contains the number of approaches and the number of unique approaches.

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• Added test to check that n_batches must be larger than or equal to the number of unique approaches. Before the user could, e.g., set n_batches = 2, but use 4 approaches and then shapr would use…

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• Updated get_default_n_batches to take into consideration the number of unique approaches that is used. This was not done before and gave inconsistency in what number shapr would reccomend and use…

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• Changed where seed is set such that it applies for both regular and combined approaches.

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• Typo

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• Added test to check that setting the seed works for combined approaches.

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• typo in test function

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• Added file to demonstrate the bugs (before the bugfix)

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• Added new test

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• Updated tests by removing n_samples

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• Added a bugfix to shapr not using the correct number of batches. Maybe not the most elegant solution.

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• Updated the demonstration script

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• Added last test and fixed lintr

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• Lint again.

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Commits on Sep 5, 2023

• Merge remote-tracking branch 'origin/master' into Lars/bugfix_n_combinations

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• styler

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• minor edits to tests

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• Merge branch 'Lars/bugfix_n_combinations' into Lars/bugfix_combined_approaches

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• simplifies comment

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• comb files ok

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• Merge master into branch

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Commits on Sep 6, 2023

• Updated bug in independence approach related to categorical features which caused shapr to crash later. Added comments when I debuged to understand what was going on. I have added some comments abo…

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• Updated bug in independence approach related to categorical features which caused shapr to crash later. Added comments when I debuged to understand what was going on. I have added some comments abo…

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• Merge branch 'Lars/bugfix_combined_approaches' of https://github.com/LHBO/shapr into Lars/bugfix_combined_approaches

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• lint warning

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Commits on Sep 7, 2023

• Lint

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• lint

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• Merge with the branch with the bugfix for the combined approaches. Note that we have to merge later again due to that we have extra roxygen2 stuff which should not be included. But let I let Martin…

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• Updated roxygen

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• Merge branch 'Lars/bugfix_get_default_n_batches' into Lars/add_MSEv_eval_criterioAdd the bugfixes related to combined approaches such that the tests of the MSEv plots become correct.

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• Added plot test functions for MSEv criterion

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Commits on Sep 8, 2023

• Ran styler

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• Updated most lintr. I disagree that variable names should be less than 30 characters. Discuss with Martin. And it was Stylr that made the changes that caused the brace_linter warnings.

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• Previous version would not test the output but rather that check that shapr would stop as n_batches was less than the length of approch.

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• Added some extra parameters to the one test function.

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• Updated some parameters in the MSEv test plots. Looked at all of them and they look to do what I want.

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• SupressMessages to run testthat::test_file without messages, and changed tha bar_plot_MSEv such that we do not get printed NULL to the console when running the test.

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• Add test images (get the same each time I run testthat::test_file()).

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• Fixed lintr and styler

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• Updated vignette with MSEv. Fixed lintr and ensured that the figures look like what they are supposed to.

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Commits on Sep 9, 2023

• updated test files after accepting new values

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• adjustments to comments and Lars' TODO-comments

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Commits on Sep 10, 2023

• update snapshot file after weight adjustment

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• cleaned up doc

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• rerun doc

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• style

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• Merge branch 'master' into Lars/bugfix_combined_approaches

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Commits on Sep 11, 2023

• Merge branch 'Lars/bugfix_combined_approaches' into Lars/bugfix_get_default_n_batches

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• Merged master into branch.

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Commits on Sep 12, 2023

• Changed to n_batches = 10 in the combined approaches, as the previous value (n_batches = 1) is not allowed anymore as it is lower than the number of unique used approaches.

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Commits on Sep 14, 2023

• Updated some messages in plot

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Commits on Sep 15, 2023

• Merged the master into this branch

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• Minor updates to make_MSEv_evaluation_criterion_plots

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• Update the manuals

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Commits on Sep 18, 2023

• Updated the MSEv text in the vignette.

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Commits on Nov 16, 2023

• Merge branch 'Lars/bugfix_get_default_n_batches' of github.com:LHBO/shapr into Lars/bugfix_get_default_n_batches

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• accept OK test changes

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• additonal Ok test files

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• change batches in test files

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• accept new files

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Commits on Nov 17, 2023

• handle issue with a breaking change update in the testthat package

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• + these

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Commits on Nov 20, 2023

• removing last (unused) input of approach

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• updating tests

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• + update setup tests/snaps

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• correcting unique length

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• update linting and vignette

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• update docs

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• fix example issue

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• temporary disable tests on older R systems

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• remove unecessary if-else test

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• data.table style on Lars's batch adjustment suggestion

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• del comment

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• lint

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• Merge branch 'Lars/bugfix_get_default_n_batches' into Lars/add_MSEv_eval_criterion

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• snaps + test adjustment

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• update plotting snaps to make tests pass

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• update vignette

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• .

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• Renamed compute_MSEv_evaluation_criterion() to compute_MSEv_eval_crit().

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• Renamed MSEv_evaluation_criterion_for_each_coalition to MSEv_eval_crit_each_comb.

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• Shorted function/variable names to less than 30 char.

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• Renamed MSEv_eval_crit_comb to MSEv_eval_crit_combination for consistency.

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Commits on Nov 21, 2023

• Added option for using Shapley weights in compute_MSEv_eval_crit()

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• Merge remote-tracking branch 'origin/master' into Lars/add_MSEv_eval_criterion

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• update snaps after name change

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• update function names in tests

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• new figure snaps

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• update function names in vignette

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• man + example bug

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• Fixed places where variable names where not updated

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• Manual updates

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• Added library(shapr) in examples.

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• Updated combined approach in make_MSEv_eval_crit_plots example to support new version.

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• Export compute_MSEv_eval_crit to make devtools::run_examples() run.

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Commits on Nov 24, 2023

• Merge branch 'Lars/add_MSEv_eval_criterion' of github.com:LHBO/shapr into Lars/add_MSEv_eval_criterion

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Commits on Nov 26, 2023

• Added support for MSEv criterion in explain().

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• Updated MSEv criterion based on feedback.

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• Added checks for MSEv criterion

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• Refactored the plot function for MSEv based on feedback

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• Updated vignette to reflect changes in MSEv criterion code.

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Commits on Nov 27, 2023

• Fixed MSEv_combination. Now taking mean of it gives MSEv and we see the weighted importance of the combination on the overall precission when plotting.

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• Removed default palette and refactored the code.

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• Updated the vignette to reflect the changes in MSEv criterion.

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• Set default MSEv values in setup() as explain_forecast() do not specify them.

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• Merge branch 'Lars/add_MSEv_eval_criterion' of github.com:LHBO/shapr into Lars/add_MSEv_eval_criterion

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• Added tests for MSEv_skip_empty_full_comb and MSEv_uniform_comb_weights. Matched the setup for other logical arguments.

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• Added test for when MSEv criterion use the Shapley kernel weights

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• Fixed bug in MSEv_plot function when specifying geom_col_width

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• Fixed tests for MSEv plot function

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• Added MSEv references

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• Added Lars as Author

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Commits on Nov 30, 2023

• Removed MSEv_skip_empty_full_comb form explain and all other functions/tests.

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• Fixed inncorrect standard deviations of the mean. Now divides by sqrt(n_explain). And better documentation.

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Commits on Dec 1, 2023

• MSEv_plots: introduced approximate CI, reduced example, improved documentation

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• Updated MSEv_plot documentation

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• Added example file for how to change the MSEv plots

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• Inserted level = 0.95 the places it where missing.

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• Added CI explanation in vignette.

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• Fix linting and stylr.

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• Updated manuals (done autmatically by devtools::run_examples())

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• Added snaps plot svg files

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Commits on Dec 8, 2023

• Merge branch 'Lars/add_MSEv_eval_criterion' of github.com:LHBO/shapr into Lars/add_MSEv_eval_criterion

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• æ ø

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• update test files

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• del unused snaps

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• typo

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• man

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• styler

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• bugfix name in testfile

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• fixing check warning of missing ... description

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• fix check note on NSE

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• Renamed make_MSEv_eval_crit_plots into plot_MSEv_eval_crit

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• Changed default confidence level to check for the number of explicands

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• Renamed the parameter level into CI_level in the plot_MSEv_eval_crit function.

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• Updated plot_MSEv_eval_crit.Rd and namespace

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• Introduced plot_type parameter in plot_MSEv_eval_crit() and updated title

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• styler

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• Updated manual

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• Updated from ifelse to if else to support NULL return

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Commits on Dec 11, 2023

• swap * + space with ~ in bquote to fix spacing in svg files

  martinju

  committed
  cca8287

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• update svg files

  martinju

  committed
  cbe0baf

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• man

  martinju

  committed
  16cfdeb

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• bugfix vignette + remove unecessary plot arguments

  martinju

  committed
  c70d947

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• fix NSE check issues

  martinju

  committed
  2f1ee6a

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