Ecosyste.ms: Issues

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GitHub / SchlossLab/mikropml issues and pull requests

#343 - Preprocessing in run_ml?

Issue - State: closed - Opened by pschloss 5 months ago - 1 comment
Labels: wontfix

#340 - Fix roxygen package doc syntax

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#339 - Factor levels in outcome column are not preserved

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: bug

#338 - Precision should be 1 when TP=1 and FP=0

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: bug

#337 - Preserve factor levels in outcome column

Pull Request - State: open - Opened by kelly-sovacool over 1 year ago

#336 - Added option to impute missing values during training

Pull Request - State: open - Opened by megancoden over 1 year ago - 4 comments

#335 - Generate docs for internal functions

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#334 - New vignette for visualizing performance and feature importance

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: documentation

#333 - Calculate balanced precision

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#332 - Link to GitHub Discussions for help

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: documentation

#330 - Calculate the area under the balanced precision-recall curve (AUBPRC)

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: feature, good first issue

#329 - Create `bootstrap_performance()` for single train/test splits

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago

#328 - roxygen2 docs: switch `@noRd` to `@keywords internal` for all internal functions

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: documentation, good first issue

#327 - Switch from {future.apply} to {furrr} where possible

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment

#326 - Report confidence interval for permutation feature importance

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#324 - Report confidence interval for permutation feature importance

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: feature

#323 - Improve description of `run_ml()` and its args

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago

#322 - Release 1.5.0

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#321 - Plot ROC & PRC curves

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#320 - Use get_partition_indices() in case weights example

Pull Request - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#319 - Extracting weights from 100 iterations and from random random forset model

Issue - State: closed - Opened by Hesham999666 almost 2 years ago - 1 comment

#314 - Fix feature importance plot

Pull Request - State: closed - Opened by kelly-sovacool almost 2 years ago - 3 comments
Labels: bug, documentation

#313 - NaN as character causes some problems

Issue - State: closed - Opened by sskoldas almost 2 years ago - 3 comments

#310 - Show example feature importance plot

Pull Request - State: closed - Opened by kelly-sovacool almost 2 years ago

#308 - meta-analysis using mikropml?

Issue - State: closed - Opened by marwa38 almost 2 years ago

#306 - Support parRF using rf hyperparams

Pull Request - State: closed - Opened by kelly-sovacool almost 2 years ago

#305 - Use hyperparams from `rf` for `parRF`

Issue - State: closed - Opened by kelly-sovacool almost 2 years ago
Labels: feature

#304 - Forward extra arguments to `caret::train()`

Pull Request - State: closed - Opened by kelly-sovacool almost 2 years ago - 1 comment

#303 - Test that the plot prints without warnings

Pull Request - State: closed - Opened by kelly-sovacool almost 2 years ago

#302 - Refactor `select_apply()`

Issue - State: open - Opened by kelly-sovacool almost 2 years ago

#301 - Impute missing values after the train/test split

Issue - State: open - Opened by kelly-sovacool almost 2 years ago
Labels: feature

#300 - Create unit test for plot_model_performance()

Pull Request - State: closed - Opened by kelly-sovacool about 2 years ago

#298 - Update tests to use the 3rd edition of testthat

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago - 4 comments

#297 - Prepare to release v1.3.0

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago - 1 comment

#296 - use which run_ml() output to plot ROC curve?

Issue - State: closed - Opened by zhq90 over 2 years ago - 2 comments

#295 - Create function to compare models with a permutation test

Pull Request - State: closed - Opened by courtneyarmour over 2 years ago - 1 comment

#294 - classification of new (and outcome unknown) samples

Issue - State: closed - Opened by fairquestion over 2 years ago - 1 comment

#293 - Improve feature importance examples

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago

#292 - Depend on R >= 4.1.0 because randomForest does now

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago

#291 - Use cv_times for repeats in trainControl

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago

#290 - Fix no-long-double test failure

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago

#289 - Prepare to release v1.2.1

Pull Request - State: closed - Opened by kelly-sovacool over 2 years ago - 1 comment

#288 - Report p-values in the feature importance dataframe

Pull Request - State: closed - Opened by kelly-sovacool almost 3 years ago - 1 comment

#287 - Report p-values for permutation importance

Issue - State: closed - Opened by kelly-sovacool almost 3 years ago
Labels: feature

#286 - Use tidy github documents

Pull Request - State: closed - Opened by kelly-sovacool almost 3 years ago

#285 - Allow kfold to be larger than the number of groups in the training set

Pull Request - State: closed - Opened by kelly-sovacool almost 3 years ago - 1 comment

#283 - Warning message about '%dorng%' vs '%dopar%' when run in parallel

Issue - State: closed - Opened by dansmith01 almost 3 years ago - 2 comments

#282 - Improve docs for the training_frac & groups options

Pull Request - State: closed - Opened by kelly-sovacool almost 3 years ago - 2 comments

#281 - Create group_partitions option & allow direct control over train/test split

Pull Request - State: closed - Opened by kelly-sovacool almost 3 years ago - 1 comment

#278 - Add parameter for custom cross-validation schemes

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago - 1 comment

#277 - Fix typo: svmRadial uses a radial kernel, not linear

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago

#276 - Refactor group_correlated_features()

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago - 2 comments

#275 - Rename branch 'master' to 'main'

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago

#274 - find_feature_importance fails for multiclass data

Issue - State: closed - Opened by alexmsalmeida about 3 years ago - 6 comments

#273 - Don't convert outcome vectors to characters in preprocess_data()

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago

#272 - Conversion of numeric outcomes to character error

Issue - State: closed - Opened by ecmaggioncalda about 3 years ago - 1 comment
Labels: bug

#271 - Providing case weights

Issue - State: closed - Opened by funnell about 3 years ago - 4 comments
Labels: feature

#270 - Link to @pschloss' ML playlist on YouTube

Pull Request - State: closed - Opened by kelly-sovacool about 3 years ago

#269 - grouped features are not always in the same order

Issue - State: closed - Opened by ecmaggioncalda about 3 years ago
Labels: bug, reprex

#268 - Need function to compare models

Issue - State: closed - Opened by pschloss about 3 years ago - 5 comments
Labels: feature

#267 - Add option for correlation method

Pull Request - State: closed - Opened by courtneyarmour over 3 years ago - 2 comments

#266 - update documentation

Pull Request - State: closed - Opened by courtneyarmour over 3 years ago - 1 comment

#265 - update get_corr_feats() to have correlation method option

Issue - State: closed - Opened by courtneyarmour over 3 years ago - 1 comment
Labels: feature

#264 - group_correlated_features() sometimes appends extra columns in R 3.6.1

Issue - State: closed - Opened by kelly-sovacool over 3 years ago
Labels: bug

#263 - Correlation threshold parameter

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 1 comment
Labels: feature

#262 - Add ROC curve example code to docs

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 3 comments
Labels: documentation, feature, good first issue

#261 - Update citation with JOSS details

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago

#260 - Acknowledge URSSI

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago
Labels: JOSS-paper

#259 - Review responses

Pull Request - State: closed - Opened by zenalapp over 3 years ago - 5 comments
Labels: JOSS-paper

#258 - Test that get_outcome_type() errors when expected

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago

#257 - Report progress in long-running functions

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago - 1 comment

#256 - Change "run ML" phrases to more appropriate ones in vignettes

Pull Request - State: closed - Opened by BTopcuoglu over 3 years ago - 4 comments

#255 - Thank Nick

Pull Request - State: closed - Opened by zenalapp over 3 years ago

#254 - Add multi-outcome unit test & note multi-label limitation

Pull Request - State: closed - Opened by zenalapp over 3 years ago - 2 comments

#253 - Use the phrase "model training" rather than "ML" where appropriate

Issue - State: closed - Opened by kelly-sovacool over 3 years ago
Labels: documentation, JOSS-paper

#252 - Test multi-outcome datasets

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 2 comments
Labels: bug, JOSS-paper

#251 - Refactor run_ml() API for future expandability

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 1 comment
Labels: wontfix, JOSS-paper

#250 - Report live updates of metrics during training

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 1 comment
Labels: feature, wontfix, JOSS-paper

#249 - Implement progress bar for long-running functions

Issue - State: closed - Opened by kelly-sovacool over 3 years ago - 3 comments
Labels: feature, JOSS-paper

#248 - Add the logo

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago

#247 - Replace spaces in outcome column with underscores

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago

#246 - Support custom groups for feature importance

Pull Request - State: closed - Opened by kelly-sovacool over 3 years ago - 1 comment

#245 - Support custom groups of features for permutation importance

Issue - State: closed - Opened by kelly-sovacool over 3 years ago
Labels: feature

#244 - Class strings cannot contain spaces in the outcome columns [JOSS review]

Issue - State: closed - Opened by JonnyTran over 3 years ago - 2 comments
Labels: bug, JOSS-paper

#243 - decision tree error

Issue - State: closed - Opened by ebechtold over 3 years ago - 4 comments

#242 - Update from model formula to x,y notation in train function

Issue - State: closed - Opened by BTopcuoglu over 3 years ago
Labels: feature

#241 - Training Webinar

Issue - State: closed - Opened by SWi1 almost 4 years ago - 2 comments

#240 - Add preprocess option to remove features that appear in N rows or fewer

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago - 1 comment

#239 - Use \dontrun{} instead of \donttest{} for Roxygen examples

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago

#238 - Clarify meaning of perf_metric_diff

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago

#237 - Check r-oldrel (currently R 3.6.2)

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago - 1 comment

#236 - Improve permutation importance calculation

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago - 1 comment

#235 - Show how to do feature importance after run_ml() if you skipped it initially

Issue - State: closed - Opened by kelly-sovacool almost 4 years ago - 1 comment
Labels: documentation

#234 - Better explain the groups param & batch effects in the intro vignette

Issue - State: open - Opened by kelly-sovacool almost 4 years ago
Labels: documentation, good first issue

#233 - Note --max-ppsize for large datasets in preprocess vignette

Issue - State: open - Opened by kelly-sovacool almost 4 years ago
Labels: documentation, good first issue

#232 - Incorporate documentation edits from Schloss Lab meeting

Pull Request - State: closed - Opened by kelly-sovacool almost 4 years ago - 1 comment

#231 - Intro vignette proof read

Issue - State: closed - Opened by pschloss almost 4 years ago
Labels: documentation

#230 - Edit hyperparameter tuning vignette

Issue - State: closed - Opened by NLesniak almost 4 years ago - 3 comments
Labels: documentation