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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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- New argument 'default_log_parms' for mean_degparms()
- 'plot.mixed.mmkin': Pass the frame argument also to residual plots,
take the 'default_log_parms' argument for 'mean_degparms' used for
constructing approximate population curves, plot population curve last
to avoid that it is covered by data
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The EFSA URL failed on winbuilder because some cookie sets a different
domain, so I am now using \href{} with the full link as link text instead
of \url{}
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The data given in previous mkin versions for "Borstel 2" (Staudenmaier
2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2"
data simply being further analysed for isomer composition by
Staudenmaier (2013).
While correcting this, the URL of the RAR published by EFSA was
updated, as the EFSA Register of Questions was replaced by the
Open EFSA portal.
This also affects the recent publication in "Environments" [1], where
these two datasets were pooled. However, the influence on the final
results can be expected to be minimal. Out of the 16 observations for
the Borstel soil, five were erroneously duplicated which just changes
the weight of the different sampling points and modifies the variance.
The conclusions of the publication are qualitative and are not
considered to be affected.
[1] https://doi.org/10.3390/environments8080071
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Evaluations with nlme, saemix and nlmixr are included
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Also adapt summary.nlmixr.mmkin to correctly handle the way
formation fractions are translated to nlmixr
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Works for the dimethenamid data, at least for FOCEI. Very little testing
yet. The summary function does not yet handle the new transformations
of formation fractions (that are in fact very old, as they were used
in the very first version of mkin). The test file has no tests yet, just
some code that may be used for testing.
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