Merge master into develop (#404)

* 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>