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Also, give some structure to the menu for selecting articles
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To ensure that tests on different platforms work on the same data, the
mixed modelling test data previosly generated in
tests/testthat/setup_script.R were generated once using the script in
inst/dataset/generation/ds_mixed.R, and are now distributed with the
package.
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- Split out llhist and parhist documentation
- Add example code for multistart
- Create a multistart vignette, because the example code fails when run
by pkgdown
- Fix multistart for the case of mkin transformations in the saem fit
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I am postponing my attempts to get the nlmixr interface to CRAN, given
some problems with nlmixr using R-devel under Windows, see
https://github.com/nlmixrdevelopment/nlmixr/issues/596
and
https://github.com/r-hub/rhub/issues/512,
which is fixed by the removal of nlmixr from the testsuite.
For the tests to be more platform independent, the biphasic mixed
effects models test dataset was defined in a way that fitting
should be more robust (less ill-defined).
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It didn't pick up the release of 1.0.3, and most of the other release
dates were duplicated.
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Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.
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The errors in the example code were in the \dontrun sections, so they
were not caught by CRAN checks. In addition, the static help files
generated with pkgdown were cached, so I noticed the errors only
after completely regenerating the documentation for version 1.0.0.
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- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest
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By depending on parallel instead of importing it, functions to set up
and stop a cluster are always available when mkin is loaded.
The use of multicore processing in mmkin on Windows is now documented in
the help file, which brings mkin closer to a version 1.0 #9.
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With a plot method. The class mixed.mmkin is currently only a virtual
class created to unify the plotting method.
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Also make the endpoints function work for saem objects.
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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.
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Improve and update docs
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Update docs
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Also commit the dontrun instruction for saemix I had wanted to commit
and switch back to devel mode for pkgdown
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instead of the orange danger color.
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saemix_data depends on a development version of saemix, see
pull request saemixdevelopment/saemixextension#2
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also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
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- Switch an example dataset in the test setup to a dataset with
replicates, adapt tests
- Skip the test for lrtest with an update specification as it does not
only fail when pkgdown generates static help pages, but also in testthat
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The likelihood ratio test method is lrtest, in addition,
methods for update and residuals were added.
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