Refresh README #335
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@IndrajeetPatil Why do we need to generate README.md from README.Rmd? |
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How can you solve #334 without using |
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I mean now the issue is solved, but it wouldn't have been without the Rmd. So I can delete it now, but, in general, I prefer generating md from Rmd. |
If we have both README.md and README.Rmd - which one is used for the intro page generation by pkgdown? If README.md - we can write the badges directly in README.md in the form just generated from .Rmd: |
PavelBal
approved these changes
Jul 18, 2022
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Yeah, I have removed the .Rmd file now. |
Yuri05
reviewed
Jul 18, 2022
Yuri05
approved these changes
Jul 18, 2022
Yuri05
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Jan 27, 2023
* Refresh README Closes Open-Systems-Pharmacology#153 Closes Open-Systems-Pharmacology#334 * remove README.Rmd * Update README.md
msevestre
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Jan 27, 2023
* Version 1.4.89 (#323) * Fixes #280 background elements defined a priori (#284) This allows to switch off grid at creation of plot configuration * Fixes #281 Fixes #282 update vignettes (#290) * Fixes #289 update news (#291) * 273 na rm (#278) * Fixes #273 NA are removed without producing warnings * Fixes #272 set transparency for molecular plots * Update line layer in scatter plots * Fix typo Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #288 create sections in reference page of doc website (#292) * Fixes #288 create sections in reference page of doc website * Remove duplicated last reference section * Export configuration output folder (#287) * Add `path` property to `ExportConfiguration` * Added argument `path` to `ExportConfiguration` Documentation generated with roxygen2 * Run styler * Fix wrong assignment of `path` property * adopt same gitattributes as other R repos in OSP (#295) * whitespace changes due to new gitattributes * Improvements to the `PlotGridConfiguration` class (#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes #274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file * also add watermark size to the enum (#297) * whitespace changes due to new gitattributes * Use utilities from ospsuite.utils (#299) To be considered once Open-Systems-Pharmacology/OSPSuite.RUtils#115 is merged. * Add `collate` directive (#296) * Fixes #301 Helper function to get lines from fold distance values (#302) * Fixes #301 Helper function to get lines from fold distance values * Update news, doc and style * Update NEWS.md * Update NEWS.md Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * 262 res vs pred (#270) * Fixes #262 update documentation of plotResVsPred * Fixes #262 res vs time functions are aliases of res vs pred functions Include plotResVsTime, ResVsTimePlotConfiguration and ResVsTimeDataMapping * res vs time classes derive from res vs pred As a consequence, they are not equal and can have different theme properties * re-document Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #304 add enum helper for ticklabels (#305) * Fixes #304 add enum helper for ticklabels * Fix typo in Pi label mapping * Fix typo in example * If ticklabels is of type expression, numeric or function use it as is If expression or function isIncluded throw an error so the assertion is necessary before isIncluded * style and document Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Prepend internal function names with a dot (#307) As per coding guidelines. Update docs for these functions as well. Closes #306 * 308 fold distance (#311) * Fixes #313 Remove badges from Website-docu, update news (#314) Co-authored-by: Yuri05 <Yuri05@github.com> * Fixes #260 legend titles are updated and can be defined in themes (#315) * Fixes #260 legend titles are updated and can be defined in themes * Remove legend and legend title reset in boxplots * Fixes #312 remove infinite values from plots (#316) * fixes #318 Update website (#319) Co-authored-by: Yuri05 <Yuri05@github.com> * Fixes #320 Website: some images not displayed (#321) Co-authored-by: Yuri05 <Yuri05@github.com> * 320 attempt2 (#322) * delete old docs folder * Fixes #320 Website: some images not displayed Co-authored-by: Yuri05 <Yuri05@github.com> Co-authored-by: Pierre Chelle <45343665+pchelle@users.noreply.github.com> Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com> Co-authored-by: Yuri05 <Yuri05@github.com> * Improvements to the `PlotGridConfiguration` class (#293) * Bump package version; update NEWS * Also update website for new package version * rest * Update appveyor.yml * Add print method for plot grid config Closes #274 * document * better example * better headers * add more aesthetic parameters for plot grid config - Add needed enums - Update NEWS for the same - Update docs - Add test - Update examples * style * caption position * bump version * Add PlotAnnotationTextSize * move enums to plot grid file * docs * Update PlotGridConfiguration.Rd * needed for vdiffr tests * move all enums to their own file * also add watermark size to the enum (#297) * Fixes #301 Helper function to get lines from fold distance values (#302) * Fixes #301 Helper function to get lines from fold distance values * Update news, doc and style * Update NEWS.md * Update NEWS.md Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #304 add enum helper for ticklabels (#305) * Fixes #304 add enum helper for ticklabels * Fix typo in Pi label mapping * Fix typo in example * If ticklabels is of type expression, numeric or function use it as is If expression or function isIncluded throw an error so the assertion is necessary before isIncluded * style and document Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * 308 fold distance (#311) * 320 attempt2 (#322) * delete old docs folder * Fixes #320 Website: some images not displayed Co-authored-by: Yuri05 <Yuri05@github.com> * Fixes #325 legend title properties from argument title are used (#328) Issue was caused because properties of R6 (Label object here) are linked if object is not cloned * Fixes #327 horizontal bars for obs vs pred plots (#331) - error is replaced in favor of ymin/ymax or xmin/xmax - dataMapping initialize method needs to explicitly redefine `x` and `y` arguments because of R partial matching (if user inputs `x="a"`, partial matching would assign "a" to `xmin` instead of `x` because `xmin` was the only argument explicitly defined) * Refresh README (#335) * Refresh README Closes #153 Closes #334 * remove README.Rmd * Update README.md * Classify vignettes on the website (#336) Closes #178 * Make `.Rbuildignore` more comprehensive (#337) * Make `.Rbuildignore` more comprehensive Get rid of `NOTE` about unexpected top-level files * Update .Rbuildignore * Update to roxygen2 7.2.1 (#339) * Format with latest version of styler (#341) * Fixes #326 legend title use plot configuration for time profile plots (#343) * Get rid of warnings and notes in R CMD check (#338) * Fixes #333 set cap width of errorbars (#344) * Fixes #333 set cap width of errorbars Currently, width is a global setting applied the same way to all error bars * Absolute cap values are now relative and width renamed to extent Renaming width to extent to prevent user confusion when used for horizontal errorbars whose caps become vertical * Fixes #333 cap extent renamed cap size and use consistent unit in pts Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * 303 obs map to shape (#351) * Fixes #303 observed data map to shape * Fixes #346 remove dynamic code * Update documentation with latest roxygen * format with styler Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #353 time profile legend guide display and order shapes (#355) * Fixes #356 display minor ticks (#357) * Fixes #356 display minor ticks * fix test Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #354 ObservedDataMapping signature consistent with TimeProdfle (#358) * Fixes #360 add linetype as internal splitting group for simulation range (#361) * Fixes #350 default obs vs pred plot use same axes limits (#365) The same option also centers residuals vs pred/time around 0 * format with {styler} (#366) * Fixes #368 Add identity in Scaling enum (#371) Also fix a typo in enum Shapes * Fixes #375 Add spellcheck * Fixes #362 introduce qq plots (#370) * Fixes #362 introduce qq plots * Remove empty y check overkill Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes #364 introduce cumulative time profile plots (#378) * 374 enum listing molecules (#380) * Fixes #375 enums listing all molecules, atoms and their configurations * Fixes #379 Synchronize theme and molecule plots * Rename Atoms and Molecules to AtomPlots and MoleculePlots * Fixes #381 Prevent log ticks from crashing plots (#382) * Fixes #387 enforce factor type to prevent crash of colorBreaks (#388) levels of character type variable is null possibly leading to null colorBreaks value * Fixes #383 histogram can plot bars as frequency (#384) * Fixes #383 histogram can plot bars as frequency * Update documentation about default values of histogram * Fixes #390 Fixes #391 observed and simulated time profiles (#393) * Fixes #392 Create method for dual axis time profile plots (#396) * Fixes #392 Create method for dual axis time profile plots * Update test plot grid snapshot to latest * Fixes #398 update documentation and website (#399) * Fixes #398 update documentation and website * Fixes #398 Update version and dev documentation * Update release documentation * Fixes #397 vignette code is run only if R version is >= 4.0 (#401) * Increment AppVeyour version (1.4=>1.5) (#402) Co-authored-by: Yuri05 <Yuri05@github.com> * merge main into develop --------- Co-authored-by: Michael Sevestre <michael@design2code.ca> Co-authored-by: Pierre Chelle <45343665+pchelle@users.noreply.github.com> Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com> Co-authored-by: Yuri05 <Yuri05@github.com>
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Closes #153
Closes #334