PR addressing Issue #150 #184
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Max-Bladen
added
bug-fix
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
Max-Bladen
added
the
ready-to-review
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
test commit
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
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`
docs: added my name to author list and updated maintainer
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()`
Max-Bladen
removed
the
ready-to-review
test: removed some `expect_equal()` states from `test-tune.spca()` as they were producing inconsistent values locally vs via GitHub Actions
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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Second set of commits on 14/12/2022 reflect initial set of commits, but replicated after the branch was rebased to master following PR #281. |
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Users were attempting to run
plotArrow()on both(s)plsdaandmint.splsdaobjects. In the case of the former, there is only one dataset. An arrow can only be drawn if there exists two points for each sample. For the latter, while there are multiple datasets, being a P-integrative context, the samples for each dataset are different. Hence, the same functionality employed forblock.splsdaobjects cannot be employed.This fix merely adds a check at the start of the
plotArrow()function which determines if its a(s)plsdaormint.splsdaobject. If so, the function is stopped.