Age | Commit message (Collapse) | Author | Files | Lines |
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Emmanuelle has made an official release to CRAN in June
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The vignette illustrates pH dependent degradation (covariate modelling)
with some detail for the parent compound.
Also, a bug in the saem method of the illparms function was fixed, which
prevented to find ill-defined parameters in cases where e.g. slopes of
covariate models have a negative estimate.
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- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release
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It took too long, and this solution method is not recommended. We are
saving 140 seconds here on my system, so more time is saved on travis.
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Also, using mkin analytical solutions for more than one observed
variable is not supported (but could be if out_values would be
reordered).
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We still need to create a parallel processing cluster _after_ creating a
compiled model that is moved to a user defined location, at least I did
not find another way to make it work. This is not a problem with
parallel processing without a cluster, which is not available on
Windows.
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In mkinmod, dll_info was not included in the returned model object
in the case that the DLL was moved to a user defined directory.
This is now fixed.
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Update platform dependent test plots
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Thanks to Sebastian Meyer for spotting it.
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Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used
as a document format in the template. In this way, the template file can
be freed from some R code and yaml options that the average user does
not have to be aware of.
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Update docs
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llquant argument, improved legend text, tests
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One printout and four plots are different using current R-devel. These
are currently skipped on CRAN. These test were run with the development
version of saemix (my branch installable_dev_version). If saemix from
CRAN is used, there are some more differences due to different error
model parameters
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https://github.com/r-lib/processx/issues/236
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Also update tests to the changes in mhmkin (see NEWS)
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Save winbuilder/CRAN check time...
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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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This will hopefully make the test pass on all relevant platforms.
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Due to an oversight, error.init was not really passed to saemix_model in
saem.mmkin. The new initial values were reverted to c(1, 1), in order to
avoid changing the test results. Initial values for error model
parameters are now shown in parplot.multistart.
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The lack of that attribute lead to a failure to calculate the BIC in
test_AIC.R on R-devel from yesterday.
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For the case of mkin transformations. This gives faster convergence,
and appears to avoid problems with numeric ODE solutions
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I do not know why the formulae for b1 and b2 on page 64 of FOCUS
kinetics (2014) were not simplified. Clearly, the term
k12 * k21 - (k12 + k1output) * k21)
can be simplified to
- k1output * k21
The test for equivalence of DFOP and SFORB fits verifies that the change
is OK. I also removed trailing whitespaces, substituted tab characters
by two whitespaces and removed indenting of text in paragraphs
describing parameters in roxygen comments to unify formatting.
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Based on parameters in the separate fits that fail the t-test.
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I think it is always preferable to be able to investigate the
saemix object returned.
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For the case of single fits and no ill-defined parameters found
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As the last update failed on travis. Now we should be more robust,
as rounding to one digit works better when parameters are
log-transformed (mkin transformations) in the output.
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That parhist name was not the brightest idea, as it does
not show histograms.
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