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* 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Deprecated `plot_*_posterior()` (#267) Following the conversation started [here](#263 (comment)), this commit moves the superseded subfunctions of `plot.SMCMallows()` into the `smc_mallows_deprecated.R` file for eventual removal.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>
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* 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> Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
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Feb 3, 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) --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
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* 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) --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
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* 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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Added
plot.SMCMallows()method + example (DRY SMC functions #114)Changed class of SMC outputs to SMCMallows (DRY SMC functions #114)
This makes proper dispatching of possible, withou having any other apparent consequences.
Adapted SMC vignette and unit tests to new
plot()method (DRY SMC functions #114)Fixed CodeFactor issue
Redundant blank line at the end of a code block should be deleted.
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 (Addedplot.SMCMallows()method #263)Added
plot.SMCMallows()method + example (DRY SMC functions #114)Changed class of SMC outputs to SMCMallows (DRY SMC functions #114)
This makes proper dispatching of possible, withou having any other apparent consequences.
Adapted SMC vignette and unit tests to new
plot()method (DRY SMC functions #114)Fixed CodeFactor issue
Redundant blank line at the end of a code block should be deleted.
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.Co-authored-by: Øystein Sørensen oystein_sorensen@hotmail.com
Fix documentation for
plot.SMCMallows()(Fix documentation forplot.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()docsReverting changes to NEWS.md
Textual change is automatically introduced by
usethis::use_dev_version().plot_*_posterior()(Deprecatedplot_*_posterior()#267)Following the conversation started
here, this commit moves the superseded subfunctions of
plot.SMCMallows()into thesmc_mallows_deprecated.Rfile 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 (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 (DRY SMC functions #114)
SMC metric defaults to footrule (DRY SMC functions #114)
SMC leap_size defaults to 1 (DRY SMC functions #114)
SMC alpha_prop_sd defaults to 0.5 (DRY SMC functions #114)
SMC alpha_max defaults to 1e6 (DRY SMC functions #114)
SMC lambda defautls to 0.1 (DRY SMC functions #114)
Update DESCRIPTION
Incremented development version.
Co-authored-by: Øystein Sørensen oystein_sorensen@hotmail.com
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