Updated deprecated ggplot2 function #286
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Maybe merge this before #283 so the develop version goes in the right order (1.2.2 to 1.2.2.9000 to 1.2.2.9001)? 😅 |
osorensen
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Mar 10, 2023
* Added `plot.SMCMallows()` method + example (#114) * Changed class of SMC outputs to SMCMallows (#114) This makes proper dispatching of possible, withou having any other apparent consequences. * Adapted SMC vignette and unit tests to new `plot()` method (#114) * Fixed CodeFactor issue Redundant blank line at the end of a code block should be deleted. * Gathererd SMC plot functions on same file (#114) This should help with future DRYing, perhaps both subfunctions should eventually be internalized? * Increment version number to 1.2.0.9004 * Updated NEWS.md * Updated build CI config file Using template from https://github.com/r-lib/actions/tree/v2-branch/examples#standard-ci-workflow * Added `plot.SMCMallows()` method (#263) * Added `plot.SMCMallows()` method + example (#114) * Changed class of SMC outputs to SMCMallows (#114) This makes proper dispatching of possible, withou having any other apparent consequences. * Adapted SMC vignette and unit tests to new `plot()` method (#114) * Fixed CodeFactor issue Redundant blank line at the end of a code block should be deleted. * Gathererd SMC plot functions on same file (#114) This should help with future DRYing, perhaps both subfunctions should eventually be internalized? * Increment version number to 1.2.0.9004 * Updated NEWS.md * Updated docs * Removed duplicated function As mentioned in the in-code comment, `scalefun()` was already defined in a different source file. * Increment version number to 1.2.1.9001 Co-authored-by: Øystein Sørensen <oystein_sorensen@hotmail.com> * Fix documentation for `plot.SMCMallows()` (#266) * Fixed links to other package functions Links were formatted wrongly assuming the package was setup to support markdown-formatted links. This fixes it. * Increment version number to 1.2.1.9002 * Reverting changes to the `compute_mallows()` docs * Reverting changes to NEWS.md Textual change is automatically introduced by `usethis::use_dev_version()`. * Deprecated `plot_*_posterior()` (#267) Following the conversation started [here](#263 (comment)), this commit moves the superseded subfunctions of `plot.SMCMallows()` into the `smc_mallows_deprecated.R` file for eventual removal. The subfunctions themselves were renamed and test units to test the deprecation warnings were written. * Matching SMC defaults to their MCMC counterparts (#269) * Updated documentation Some text were taken from the original implementation and make no longer sense. * Matched SMC defaults with their original counterparts (#114) * SMC metric defaults to footrule (#114) * SMC leap_size defaults to 1 (#114) * SMC alpha_prop_sd defaults to 0.5 (#114) * SMC alpha_max defaults to 1e6 (#114) * SMC lambda defautls to 0.1 (#114) * Update DESCRIPTION Incremented development version. Co-authored-by: Øystein Sørensen <oystein_sorensen@hotmail.com> * Added changes from PR #269 to NEWS.md Those are important to mention, since they technically break backwards compatibility. I forgot to do that on he PR itself, thankfully there's a second chance. :) * Develop (#271) (#273) * Added `plot.SMCMallows()` method + example (#114) * Changed class of SMC outputs to SMCMallows (#114) This makes proper dispatching of possible, withou having any other apparent consequences. * Adapted SMC vignette and unit tests to new `plot()` method (#114) * Fixed CodeFactor issue Redundant blank line at the end of a code block should be deleted. * Gathererd SMC plot functions on same file (#114) This should help with future DRYing, perhaps both subfunctions should eventually be internalized? * Increment version number to 1.2.0.9004 * Updated NEWS.md * Updated build CI config file Using template from https://github.com/r-lib/actions/tree/v2-branch/examples#standard-ci-workflow * Added `plot.SMCMallows()` method (#263) * Added `plot.SMCMallows()` method + example (#114) * Changed class of SMC outputs to SMCMallows (#114) This makes proper dispatching of possible, withou having any other apparent consequences. * Adapted SMC vignette and unit tests to new `plot()` method (#114) * Fixed CodeFactor issue Redundant blank line at the end of a code block should be deleted. * Gathererd SMC plot functions on same file (#114) This should help with future DRYing, perhaps both subfunctions should eventually be internalized? * Increment version number to 1.2.0.9004 * Updated NEWS.md * Updated docs * Removed duplicated function As mentioned in the in-code comment, `scalefun()` was already defined in a different source file. * Increment version number to 1.2.1.9001 Co-authored-by: Øystein Sørensen <oystein_sorensen@hotmail.com> * Fix documentation for `plot.SMCMallows()` (#266) * Fixed links to other package functions Links were formatted wrongly assuming the package was setup to support markdown-formatted links. This fixes it. * Increment version number to 1.2.1.9002 * Reverting changes to the `compute_mallows()` docs * Reverting changes to NEWS.md Textual change is automatically introduced by `usethis::use_dev_version()`. * Deprecated `plot_*_posterior()` (#267) Following the conversation started [here](#263 (comment)), this commit moves the superseded subfunctions of `plot.SMCMallows()` into the `smc_mallows_deprecated.R` file for eventual removal. The subfunctions themselves were renamed and test units to test the deprecation warnings were written. * Matching SMC defaults to their MCMC counterparts (#269) * Updated documentation Some text were taken from the original implementation and make no longer sense. * Matched SMC defaults with their original counterparts (#114) * SMC metric defaults to footrule (#114) * SMC leap_size defaults to 1 (#114) * SMC alpha_prop_sd defaults to 0.5 (#114) * SMC alpha_max defaults to 1e6 (#114) * SMC lambda defautls to 0.1 (#114) * Update DESCRIPTION Incremented development version. Co-authored-by: Øystein Sørensen <oystein_sorensen@hotmail.com> * Added changes from PR #269 to NEWS.md Those are important to mention, since they technically break backwards compatibility. I forgot to do that on he PR itself, thankfully there's a second chance. :) Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Setting Cpp version to 17 (#276) * Updated CI YAMLs, fixed lints (#278) * Updated linter CI (#270) Based on https://github.com/r-lib/actions/tree/v2/examples#lint-workflow * Removed some style rules * Fixed linting on functions and tests * Minor rewording of SMC vignette Resolved lint issues, replaced mentions of SMC-Mallows as an extension to BayesMallows (since it's now part of the package). * Updated test CI (#270) Based on https://github.com/r-lib/actions/tree/v2/examples#test-coverage-workflow * Explicitly loading package on SMC vignette Also, excludes that line from the linter check * Fixed Cpp issue (#280) * Updated ggplot2 code (#286) * issue 257 (#283) * Created validation function (#257) * DRYing SMC aug_method checks (#257) * Adjusted test unit expectations (#257) * Added unit test for internal C++ function (#257) * Increment version number to 1.2.1.9004 * Updated NEWS.md * Removed blank line (CodeFactor nag) * Updated package version to match master + build * Reinstaing seed for C++ test The `leapandshift.cpp` file contains random tests that depend on the seed. --------- Co-authored-by: Øystein Sørensen <oystein_sorensen@hotmail.com> * Improved SMC post-processing functions (#287) * Improved validation, docs of post-processing functions (#262) - Improved validation, docs of smc_mallows(). This is mostly to be a bit safer, since this function is not exported. - Improved validation, docs of remaining SMC post-processing function The validation adds a package dependency on methods, which should be fine since this is a base package. * Added examples to post-processing functions (#262) Used code from the vignette, then reduced `iter` and `N` for faster computing. * Added tests for SMC post-processing functions (#262) * Updated NEWS.md * Increment version number to 1.2.2.9002 * Added heat_plot function #255 (#288) * Added heat_plot function #255 * Fixed variable bindings * Updated NEWS.md and incremented development version * Fixing linter issues --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
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Should solve #285.