mkin/man/mkinpredict.Rd, branch v1.0.3Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.0.32020-11-07T11:54:58ZCreate saem generic for fitting saemix models2020-11-07T11:54:58ZJohannes Rankejranke@uni-bremen.de2020-11-07T11:54:58Zurn: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 robust2020-11-07T10:54:13ZJohannes Rankejranke@uni-bremen.de2020-11-07T10:54:13Zurn:sha1:cda47972e2b6a9610e3118dcd2270d7a1c76de3d
Also, exclude the saemix function when loading saemix in the example
code, to prevent overriding our generic
Improve documentation, now using a spell checker2020-05-12T08:58:25ZJohannes Rankejranke@uni-bremen.de2020-05-12T08:58:25Zurn:sha1:01284e456dc6df8e064a7a42f194fcd81d9ce7a1Avoid merge() and data.frame() in cost function2020-05-11T03:18:32ZJohannes Rankejranke@uni-bremen.de2020-05-11T03:15:19Zurn: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 solutions2020-05-09T19:18:42ZJohannes Rankejranke@uni-bremen.de2020-05-09T19:18:42Zurn:sha1:efab37957381919c21d874906ce870f4941c760a
This increases performance up to a factor of five!
Another overhaul of analytical solutions2020-05-07T20:14:19ZJohannes Rankejranke@uni-bremen.de2020-05-07T20:13:33Zurn:sha1:92bd33824bde6b6b21bfc7e30953092a74d3cce5
Still in preparation for analytical solutions of coupled models
Change implementation of analytical solutions2020-05-06T19:33:12ZJohannes Rankejranke@uni-bremen.de2020-05-06T19:33:12Zurn:sha1:1195dfc8bdbf7c131d6c6ec30fedbbe746af1bee
Preparing for symbolic solutions for more than one compound
First nlme fits for models with a metabolite2020-03-30T12:03:51ZJohannes Rankejranke@uni-bremen.de2020-03-30T12:03:51Zurn:sha1:405cde11f9f26fcab0742e84c110cf3dcb2a4c1fUse roxygen for functions and methods2019-10-25T00:03:54ZJohannes Rankejranke@uni-bremen.de2019-10-24T22:37:42Zurn:sha1:0a3eb0893cb4bd1b12f07a79069d1c7f5e991495Make mkinpredict generic and write a method for fits2018-09-18T13:15:55ZJohannes Rankejranke@uni-bremen.de2018-09-18T13:15:55Zurn:sha1:850aa313ba60c7b784d96cfdc8d4c22f2beb661a