Release/1.5.2

[kylebaron]

mrgsolve 1.5.2

• Add $EVENT block for writing code related to dosing or other events that
  are implemented through model code rather than the data set (Add $EVENT block #1230).

• Add evt::reset() and evt::reset(self) functions under the evtools
  plugin; these reset the compartments in a model; overloaded functions are
  also provided to reset and dose with bolus or infusion (Add reset functions to evtools #1222).

• Completed dosing functionality in evtools plugin; use evt::addl() to
  schedule additional doses through an evt::ev object; use evt::ii() to
  set the dosing interval; use evt::ss() to advance the pharmacokinetic
  system to steady state just prior to dosing; evt::cmt() sets the compartment
  number; evt::amt() sets the dose amount; evt::rate() sets the infusion
  rate; see the user guide for the specific signatures that are available
  (Fill out evtools function set for dosing #1227).

• Add evtools model to modlib(), illustrating how to implement dosing
  regimens from inside the model a few different ways (Add $EVENT block #1230).

• Added more comprehensive checking for duplicate blocks in a model file;
  duplicate blocks are always handled when allowed; an error message is always
  issued when duplicates are not allowed (Check spec for duplicate blocks and allow multiple $PLUGIN #1238).

• Code to audit $ODE (or $DES) code, looking for an equation for every
  model compartment was refactored to use a common approach for both traditional
  models and models written with the nm-vars plugin; regardless of approach,
  the user will be warned if mrgsolve does not detect code relevant to every
  model compartment; the audit system can be bypassed by including the
  @!audit block option to $ODE (Refactor audit #1235).

• The autodec plugin was lightly refactored to avoid false positive detection
  of variables declared as double; plans are in place to narrow the
  scope of what is detected for declaration in future releases (Refactor autodec cpp variable discovery #1234).

• R help files (.Rd) reviewed and revised for consistency and formatting
  (General updates to Rd documentation #1246).

[kylebaron]

win-devel

* using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck'
* using R Under development (unstable) (2024-10-14 r87233 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* DONE
Status: OK

rhub windows

* using log directory 'D:/a/extravertive-amenable-puppy-mrgsolve/extravertive-amenable-puppy-mrgsolve/check/mrgsolve.Rcheck'
* using R Under development (unstable) (2024-10-13 r87228 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)

[kylebaron]

@kyleam I've seen some people ignore this when building the package, but it looks like the file is allowed per WRE. Any thoughts?

[kyleam]

My understanding:

• LICENSE: can be included in the package but should not be the full license

  https://cran.r-project.org/doc/manuals/R-exts.html#Licensing

  Whereas you should feel free to include a license file in your source distribution, please do not arrange to install yet another copy of the GNU COPYING [...]. Since files named LICENSE or LICENCE will be installed, do not use these names for standard license files. To include comments about the licensing rather than the body of a license, use a file named something like LICENSE.note.

• some other file (e.g., LICENSE.md) can specify the full license but should be excluded via .Rbuildignore

Summary from https://r-pkgs.org/license.html#key-files:

• As described above, the LICENSE file is used in one of two ways. Some licenses are templates that require additional details to be complete in the LICENSE file. The LICENSE file can also contain the full text of non-standard and non-open source licenses. You are not permitted to include the full text of standard licenses.

• LICENSE.md includes a copy of the full text of the license. All open source licenses require a copy of the license to be included, but CRAN does not permit you to include a copy of standard licenses in your package, so we also use .Rbuildignore to make sure this file is not sent to CRAN.

---

For mrgsolve's case, I think you could rename this new file (with the full license text) to something else and add it to .Rbuildignore. With the current format (which isn't markdown), COPYING would be a standard name. Or, if you wanted to use markdown format, usethis has a markdown-formatted copy here. You could copy that to LICENSE.md or pull it in with usethis::use_gpl_license(version = 2).

[kylebaron]

Thanks, @kyleam. Main motivation here is to get the license registered with github. I nuked the LICENSE file and dropped that from .Rbuildignore. Then, ran the usethis command which added LICENSE.md with appropriate ignore. I believe this will still be recognized by github.

[kylebaron]

Space added from usethis workflow.

[kylebaron]

R-hub run:
https://github.com/metrumresearchgroup/mrgsolve/actions/runs/11387815754