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Version 1.0
Version 1.1
…armacology/develop Version 1.3
* Fixes Open-Systems-Pharmacology#280 background elements defined a priori (Open-Systems-Pharmacology#284) This allows to switch off grid at creation of plot configuration * Fixes Open-Systems-Pharmacology#281 Fixes Open-Systems-Pharmacology#282 update vignettes (Open-Systems-Pharmacology#290) * Fixes Open-Systems-Pharmacology#289 update news (Open-Systems-Pharmacology#291) * 273 na rm (Open-Systems-Pharmacology#278) * Fixes Open-Systems-Pharmacology#273 NA are removed without producing warnings * Fixes Open-Systems-Pharmacology#272 set transparency for molecular plots * Update line layer in scatter plots * Fix typo Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com> * Fixes Open-Systems-Pharmacology#288 create sections in reference page of doc website (Open-Systems-Pharmacology#292) * Fixes Open-Systems-Pharmacology#288 create sections in reference page of doc website * Remove duplicated last reference section * Export configuration output folder (Open-Systems-Pharmacology#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 (Open-Systems-Pharmacology#295) * whitespace changes due to new gitattributes * Improvements to the `PlotGridConfiguration` class (Open-Systems-Pharmacology#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 Open-Systems-Pharmacology#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 (Open-Systems-Pharmacology#297) * whitespace changes due to new gitattributes * Use utilities from ospsuite.utils (Open-Systems-Pharmacology#299) To be considered once Open-Systems-Pharmacology/OSPSuite.RUtils#115 is merged. * Add `collate` directive (Open-Systems-Pharmacology#296) * Fixes Open-Systems-Pharmacology#301 Helper function to get lines from fold distance values (Open-Systems-Pharmacology#302) * Fixes Open-Systems-Pharmacology#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 (Open-Systems-Pharmacology#270) * Fixes Open-Systems-Pharmacology#262 update documentation of plotResVsPred * Fixes Open-Systems-Pharmacology#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 Open-Systems-Pharmacology#304 add enum helper for ticklabels (Open-Systems-Pharmacology#305) * Fixes Open-Systems-Pharmacology#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 (Open-Systems-Pharmacology#307) As per coding guidelines. Update docs for these functions as well. Closes Open-Systems-Pharmacology#306 * 308 fold distance (Open-Systems-Pharmacology#311) * Fixes Open-Systems-Pharmacology#313 Remove badges from Website-docu, update news (Open-Systems-Pharmacology#314) Co-authored-by: Yuri05 <Yuri05@github.com> * Fixes Open-Systems-Pharmacology#260 legend titles are updated and can be defined in themes (Open-Systems-Pharmacology#315) * Fixes Open-Systems-Pharmacology#260 legend titles are updated and can be defined in themes * Remove legend and legend title reset in boxplots * Fixes Open-Systems-Pharmacology#312 remove infinite values from plots (Open-Systems-Pharmacology#316) * fixes Open-Systems-Pharmacology#318 Update website (Open-Systems-Pharmacology#319) Co-authored-by: Yuri05 <Yuri05@github.com> * Fixes Open-Systems-Pharmacology#320 Website: some images not displayed (Open-Systems-Pharmacology#321) Co-authored-by: Yuri05 <Yuri05@github.com> * 320 attempt2 (Open-Systems-Pharmacology#322) * delete old docs folder * Fixes Open-Systems-Pharmacology#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>
…acology#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 Open-Systems-Pharmacology#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
… fold distance values (Open-Systems-Pharmacology#302) * Fixes Open-Systems-Pharmacology#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>
…pen-Systems-Pharmacology#305) * Fixes Open-Systems-Pharmacology#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>
* delete old docs folder * Fixes Open-Systems-Pharmacology#320 Website: some images not displayed Co-authored-by: Yuri05 <Yuri05@github.com>
…ment title are used (Open-Systems-Pharmacology#328) Issue was caused because properties of R6 (Label object here) are linked if object is not cloned
…lots (Open-Systems-Pharmacology#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 Closes Open-Systems-Pharmacology#153 Closes Open-Systems-Pharmacology#334 * remove README.Rmd * Update README.md
* Make `.Rbuildignore` more comprehensive Get rid of `NOTE` about unexpected top-level files * Update .Rbuildignore
…on for time profile plots (Open-Systems-Pharmacology#343)
…Systems-Pharmacology#344) * Fixes Open-Systems-Pharmacology#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 Open-Systems-Pharmacology#333 cap extent renamed cap size and use consistent unit in pts Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
* Fixes Open-Systems-Pharmacology#303 observed data map to shape * Fixes Open-Systems-Pharmacology#346 remove dynamic code * Update documentation with latest roxygen * format with styler Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
…-Pharmacology#357) * Fixes Open-Systems-Pharmacology#356 display minor ticks * fix test Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
…sistent with TimeProdfle (Open-Systems-Pharmacology#358)
…g group for simulation range (Open-Systems-Pharmacology#361)
… axes limits (Open-Systems-Pharmacology#365) The same option also centers residuals vs pred/time around 0
…n-Systems-Pharmacology#371) Also fix a typo in enum Shapes
…Pharmacology#370) * Fixes Open-Systems-Pharmacology#362 introduce qq plots * Remove empty y check overkill Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
…lCheck Fixes Open-Systems-Pharmacology#375 Add spellcheck
* Fixes Open-Systems-Pharmacology#375 enums listing all molecules, atoms and their configurations * Fixes Open-Systems-Pharmacology#379 Synchronize theme and molecule plots * Rename Atoms and Molecules to AtomPlots and MoleculePlots
…ash of colorBreaks (Open-Systems-Pharmacology#388) levels of character type variable is null possibly leading to null colorBreaks value
…ncy (Open-Systems-Pharmacology#384) * Fixes Open-Systems-Pharmacology#383 histogram can plot bars as frequency * Update documentation about default values of histogram
… observed and simulated time profiles (Open-Systems-Pharmacology#393)
…profile plots (Open-Systems-Pharmacology#396) * Fixes Open-Systems-Pharmacology#392 Create method for dual axis time profile plots * Update test plot grid snapshot to latest
…pen-Systems-Pharmacology#399) * Fixes Open-Systems-Pharmacology#398 update documentation and website * Fixes Open-Systems-Pharmacology#398 Update version and dev documentation * Update release documentation
Co-authored-by: Yuri05 <Yuri05@github.com>
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@msevestre should solve the merge conflicts with the last PR. |
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