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2021-08-04Improve AIC table in vignetteJohannes Ranke11-59/+73
2021-07-29Add citations to the DESCRIPTIONJohannes Ranke4-7/+17
2021-07-29Go back to 1.0.x version, update docsJohannes Ranke25-95/+103
2021-07-29Merge branch 'master' into nlmixrJohannes Ranke5-43/+36
2021-07-29Add publication to README, update docsJohannes Ranke5-43/+36
2021-07-27Fix dimethenamid vignette problems and update docsJohannes Ranke45-1072/+1131
2021-07-27Merge branch 'master' into nlmixrJohannes Ranke23-7/+7
2021-07-27Publication date for 1.0.4 in NEWS, update docsJohannes Ranke24-8/+8
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke55-9317/+8609
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Try explicit R version for travisJohannes Ranke1-1/+1
2021-07-23Update travis config, attempting to get R 4.1.0Johannes Ranke1-2/+0
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke6-92/+58
2021-07-23Update vdiffr tests for version 1.0Johannes Ranke40-9110/+5248
2021-07-23Fix travis configJohannes Ranke1-0/+4
to use up to date versions of nlme, covr and devtools
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke24-20/+2349
Evaluations with nlme, saemix and nlmixr are included
2021-06-23Test log parameters by default when deriving saemix starting parametersJohannes Ranke1-1/+1
2021-06-23Fix documentation of default random effects for nlme.mmkinJohannes Ranke1-4/+3
2021-06-22Update development version of online docsJohannes Ranke8-9289/+1019
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

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