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PR addressing Issue #150 #184
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Commits on Mar 9, 2022
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Commits on Mar 13, 2022
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The file allows for testing of the `plotArrow()` function. Two included tests check for general functionality on DIABLO objects as well as inability to function on `(mint).(s)plsda` objects
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Commits on Apr 26, 2022
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Commits on Sep 14, 2022
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Merge remote-tracking branch 'bioc/master'
$MAINTAINER_NAME authored and $MAINTAINER_NAME committedSep 14, 2022 Configuration menu - View commit details
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Commits on Sep 15, 2022
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fix: `plotVar()` can now utilise `block.pls` and `block.spls` objects which have a single Y feature (ie. (s)PLS1)
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fix: predict function has updated error messages for when feature sets are different or in different order
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refactor: cleaned output of `test_that` tests to increase ease of debugging
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Commits on Sep 19, 2022
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fix: resolved issue preventing `perf()` from properly accounting for near-zero-variance features
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Commits on Sep 22, 2022
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feat: added `plot.graph` parameter to network to allow user control over whether to plot the network or just return the output. Either way, the returned object is the same
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fix: if `validation = "loo"` in `tune.block.splsda()`, the parameter `n` would not be set. moved the lines which define `n` to outside of the `if(validation= "Mfold")` statement so its run in all cases. Additionally, increased the specificity of some warnings and errors in this function
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Commits on Sep 26, 2022
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refactor: removed depreciated `plot.tune.splsda()`. Reduces package clutter and document repetition
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Commits on Oct 6, 2022
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tests: increased suffix length in `plotLoadings()` label-length check
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Commits on Nov 8, 2022
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Commits on Nov 14, 2022
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* Fix for Issue #264 fix: updating `set-output` commands in `Get R/Bioc versions` action
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Commits on Nov 15, 2022
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Commits on Nov 17, 2022
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fix: improved nzv feature handling for block contexts, particularly via `auroc()` Filtration applied more consistently via `Check.entry.wrapper.mint.block()` . Additional failsafe added here for zero variance features. `predict()` also now checks to see if filtration has been applied to prevent it applying filtering twice. tests: adjusted new test to ensure it passes
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Commits on Nov 22, 2022
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fix: changed the depreciated `size` parameter to `linewidth` and changed `aes_string()` to `aes()` fix: additional `aes_string()` call changed to `aes()` fix: changing `aes_string()` to `aes()` introduced error. Adjusted `geom_path` calls so X and Y vectors are appropriately set refactor: removed some commented lines tests: added test for `plotIndiv.mint.plsda()` with `ellipse = TRUE`
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Commits on Nov 27, 2022
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docs: added my name to author list and updated maintainer
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Commits on Dec 6, 2022
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PR addressing Issue #275 (#276)
refactor: adjusted order of processes to increase efficiency in `repeat_cv_j()` within `tune.spca()` enhance: added safety catch for NAs provided to `tune.spca()`. It replaces NAs with 0 and notifies user of the change test: added new test file for `tune.spca()`
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Commits on Dec 8, 2022
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PR addressing Issue #172 (#177)
`perf()` now only runs T-test when `nrepeat` >= 3. Notifies user on unreliable results if `nrepeat` < 3. New `test` file for `perf()` functions to maintain coverage
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PR addressing Issue #43 (#191)
Homogenised way in which `tune.mint.splsda()` and `perf.mint.splsda()` calculate BER, such that now both use weighted average of BER across studies. Added unit tests to ensure this homogenity
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test: removed some `expect_equal()` states from `test-tune.spca()` as they were producing inconsistent values locally vs via GitHub Actions
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Commits on Dec 13, 2022
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PR addressing Issue #280 (#281)
build: added explicit global definition for `setNames()`. Resolves NOTE in R-CMD-Check build: removed `middle` parameter from Al Abadi's reference in DESCRIPTION
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The file allows for testing of the `plotArrow()` function. Two included tests check for general functionality on DIABLO objects as well as inability to function on `(mint).(s)plsda` objects
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