mkin/R/mkinpredict.R, branch v1.0.3 Fitting kinetic models to chemical degradation data (also on github) https://erac.jrwb.de/mkin/atom?h=v1.0.3 2020-12-09T20:35:02Z Make saem using mkinpredict work again 2020-12-09T20:35:02Z Johannes Ranke jranke@uni-bremen.de 2020-12-09T20:29:18Z urn:sha1:b8b60ef92c605e862294fd29c51e20e31e0ded81 I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken. Attempt to be more failsafe in saemix runs 2020-12-07T09:49:31Z Johannes Ranke jranke@uni-bremen.de 2020-12-07T09:49:31Z urn:sha1:d3531ffa0d1f190920174105facf799dd6c3a851 Improved way to have persistent DLLs for mkinmod 2020-11-27T20:19:19Z Johannes Ranke jranke@uni-bremen.de 2020-11-27T17:35:56Z urn:sha1:1e3fd1bef2a0ec1c8b73fcfefdd62fd3463bc87c Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package. Support storing mkinmod compiled code as CFunc objects 2020-11-24T00:46:57Z Johannes Ranke jranke@uni-bremen.de 2020-11-20T18:43:46Z urn:sha1:503441b0a958c1df50df0ee7cfc3bde4ea1b1865 With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13 Create saem generic for fitting saemix models 2020-11-07T11:54:58Z Johannes Ranke jranke@uni-bremen.de 2020-11-07T11:54:58Z urn:sha1:2e37905a7bf0d72751ee7326ef05a268989e49b2 The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm. Make deSolve predictions within saemix robust 2020-11-07T10:54:13Z Johannes Ranke jranke@uni-bremen.de 2020-11-07T10:54:13Z urn:sha1:cda47972e2b6a9610e3118dcd2270d7a1c76de3d Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic Add comment 2020-05-18T10:11:13Z Johannes Ranke jranke@uni-bremen.de 2020-05-18T10:11:13Z urn:sha1:f345762ddcdac65b0d565c7a622d32c1f849e7c7 Improve documentation, now using a spell checker 2020-05-12T08:58:25Z Johannes Ranke jranke@uni-bremen.de 2020-05-12T08:58:25Z urn:sha1:01284e456dc6df8e064a7a42f194fcd81d9ce7a1 Avoid merge() and data.frame() in cost function 2020-05-11T03:18:32Z Johannes Ranke jranke@uni-bremen.de 2020-05-11T03:15:19Z urn:sha1:234c9059a95e104917e488a6ddd2313234a96cdc also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette. Avoid the call to merge for analytical solutions 2020-05-09T19:18:42Z Johannes Ranke jranke@uni-bremen.de 2020-05-09T19:18:42Z urn:sha1:efab37957381919c21d874906ce870f4941c760a This increases performance up to a factor of five!