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2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke11-149/+243
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-16Translate formation fractions to nlmixr languageJohannes Ranke4-12/+223
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.
2021-06-12Small cosmeticsJohannes Ranke4-13/+36
2021-06-11Fix package name for travis config...Johannes Ranke1-1/+1
2021-06-11Fix travis syntaxJohannes Ranke1-1/+4
2021-06-11Add packages necessary for shell commands on travisJohannes Ranke1-1/+1
2021-06-11Attempt to satisfy nlme version requirement on travisJohannes Ranke1-0/+1
2021-06-11Add system requirements for symengine on TravisJohannes Ranke1-0/+1
nlmixr depends on symengine
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke62-571/+15632
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke20-115/+1209
- All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished
2021-04-21Merge branch 'master' into saemixJohannes Ranke134-374/+445
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke26-143/+158
2021-03-31Bug fix in plot.mkinfitJohannes Ranke128-248/+327
In residual plots, use xlab and xlim if appropriate
2021-03-20Fix mkin calculation of saemix residualsJohannes Ranke1-1/+1
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke6-6/+31
2021-03-16Convenience option to set nbiter.saemixJohannes Ranke1-1/+5
2021-03-09Some improvements for borderline casesJohannes Ranke52-3926/+4040
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-24Merge branch 'master' into saemixJohannes Ranke2-3/+3
2021-02-24Clarify version status in NEWSJohannes Ranke3-4/+4
2021-02-24Merge branch 'master' into saemixJohannes Ranke17-12/+36
2021-02-24Rebuild docsJohannes Ranke15-11/+25
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke6-5/+15
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke4-5/+5
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-18Merge branch 'master' into saemixJohannes Ranke13-135/+96
2021-02-15Don't let pkgdown add release datesJohannes Ranke4-99/+57
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated.
2021-02-15Update README.htmlJohannes Ranke1-2/+3
2021-02-15Correct grant numbers in README, update docsJohannes Ranke9-35/+37
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke183-739/+1020
2021-02-15Merge branch 'master' into saemixJohannes Ranke201-1096/+1551
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke202-1097/+1553
Also bump version to 1.0.3.
2021-02-13Update static docsJohannes Ranke2-6/+16
2021-02-13Structure NEWS entryJohannes Ranke1-0/+4
2021-02-13Rebuild docsJohannes Ranke1-1/+1
2021-02-13Update docsJohannes Ranke11-41/+49
2021-02-13Merge branch 'master' into saemixJohannes Ranke20-30/+62
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Post-release update of README.htmlJohannes Ranke1-2/+15
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke19-24/+43
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke58-3550/+4938
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke5-15/+18
Platform dependence also revealed after upgrade to bullseye
2021-02-06Update static docsJohannes Ranke2-90/+91
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke5-18/+9
Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset, as this is platform dependent. After the upgrade, the fit converges on this system as well, although neither ATLAS is used, nor R was configured disabling long doubles (these were the conditions under which the tests failed on CRAN).
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke42-217/+266
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.
2021-02-04Update README.htmlJohannes Ranke1-40/+2
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke199-3097/+4966
- 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
2021-01-25Update visual testsJohannes Ranke3-1895/+1895
2021-01-25Some more plotting improvementsJohannes Ranke3-8/+8
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke36-58/+62
See NEWS.md. Closes #12
2021-01-22Switch to the master branch of saemix develJohannes Ranke1-1/+1
2021-01-22We do not need to suppress saemix plots any moreJohannes Ranke2-16/+1
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM.
2021-01-11Rebuild docsJohannes Ranke14-73/+97

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