mkin/man/saemix.Rd, branch v1.2.9Fitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=v1.2.92020-11-07T11:54:58ZCreate 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
Make saemix an S3 generic in this package2020-11-06T11:39:34ZJohannes Rankejranke@uni-bremen.de2020-11-06T11:39:34Zurn:sha1:fcf06c40ec314e91ad3fdae3392f008509d70b2e
This commit also defined saemix.mmkin for mmkin row objects.
This works fine, but if we set the class of the returned object
to c("saemix.mmkin", "saemix"), it is not an S4 class any more
which make it impossible to use saemix functions on it.
Fast analytical solutions for saemix, update.mmkin2020-11-05T23:03:29ZJohannes Rankejranke@uni-bremen.de2020-11-05T23:03:29Zurn:sha1:b5b446b718b15ccaae5b197e147fc1358f0f564e
Also, use logit transformation for g and for solitary formation
fractions, addressing #10.
Update dynamic docs2020-11-04T08:50:05ZJohannes Rankejranke@uni-bremen.de2020-11-04T08:50:05Zurn:sha1:91ef22b6c98b96a9954dfe0a9914c45b41ce2af4More gentle example for saemix with combined error model2020-10-15T12:55:55ZJohannes Rankejranke@uni-bremen.de2020-10-15T12:55:55Zurn:sha1:a9c7a1a8322567e9406a59ba0a4f910b89bd05e6Get current nlme version from CRAN on Travis2020-10-15T11:17:45ZJohannes Rankejranke@uni-bremen.de2020-10-15T11:17:45Zurn:sha1:f4f6cc84d32e135b03300bf78578f1981c489bfe
Also commit the dontrun instruction for saemix I had wanted to commit
and switch back to devel mode for pkgdown
Updating docs of current dev version2020-10-15T10:27:40ZJohannes Rankejranke@uni-bremen.de2020-10-15T10:27:40Zurn:sha1:272aba066f0d7502e319b7e7f14009318cd44348Reintroduce saemix helper functions2020-10-15T08:25:48ZJohannes Rankejranke@uni-bremen.de2020-10-15T08:25:48Zurn:sha1:954f7514144a281b73e9b47ac88a6b13e8799f31Fix issues for release2020-10-08T07:31:35ZJohannes Rankejranke@uni-bremen.de2020-10-08T07:31:35Zurn:sha1:bc3825ae2d12c18ea3d3caf17eb23c93fef180b8