Age | Commit message (Collapse) | Author | Files | Lines | |
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2021-09-16 | Merge branch 'master' into nlmixr | Johannes Ranke | 16 | -97/+65 | |
2021-09-15 | Fix Open EFSA URL, changelog for 1.0.5v1.0.5 | Johannes Ranke | 4 | -6/+10 | |
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{} | |||||
2021-09-15 | Update test result to corrected data, version bump | Johannes Ranke | 6 | -28/+21 | |
2021-09-15 | Use my drat repo for saemix master | Johannes Ranke | 1 | -3/+1 | |
2021-09-15 | Try to make remotes::install_github work again | Johannes Ranke | 1 | -0/+1 | |
2021-09-15 | Update link for travis badge | Johannes Ranke | 2 | -2/+2 | |
2021-09-15 | Correction of the dimethenamid dataset | Johannes Ranke | 3 | -18/+10 | |
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 | |||||
2021-08-04 | Improve AIC table in vignette | Johannes Ranke | 11 | -59/+73 | |
2021-07-29 | Add citations to the DESCRIPTION | Johannes Ranke | 4 | -7/+17 | |
2021-07-29 | Go back to 1.0.x version, update docs | Johannes Ranke | 25 | -95/+103 | |
2021-07-29 | Merge branch 'master' into nlmixr | Johannes Ranke | 5 | -43/+36 | |
2021-07-29 | Add publication to README, update docs | Johannes Ranke | 5 | -43/+36 | |
2021-07-27 | Fix dimethenamid vignette problems and update docs | Johannes Ranke | 45 | -1072/+1131 | |
2021-07-27 | Merge branch 'master' into nlmixr | Johannes Ranke | 23 | -7/+7 | |
2021-07-27 | Publication date for 1.0.4 in NEWS, update docs | Johannes Ranke | 24 | -8/+8 | |
2021-07-23 | Merge branch 'master' into nlmixr | Johannes Ranke | 55 | -9317/+8609 | |
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object | |||||
2021-07-23 | Try explicit R version for travis | Johannes Ranke | 1 | -1/+1 | |
2021-07-23 | Update travis config, attempting to get R 4.1.0 | Johannes Ranke | 1 | -2/+0 | |
2021-07-23 | Rerun tests, use current vdiffr on travis | Johannes Ranke | 6 | -92/+58 | |
2021-07-23 | Update vdiffr tests for version 1.0 | Johannes Ranke | 40 | -9110/+5248 | |
2021-07-23 | Fix travis config | Johannes Ranke | 1 | -0/+4 | |
to use up to date versions of nlme, covr and devtools | |||||
2021-07-23 | Some example evaluations of dimethenamid data | Johannes Ranke | 24 | -20/+2349 | |
Evaluations with nlme, saemix and nlmixr are included | |||||
2021-06-23 | Test log parameters by default when deriving saemix starting parameters | Johannes Ranke | 1 | -1/+1 | |
2021-06-23 | Fix documentation of default random effects for nlme.mmkin | Johannes Ranke | 1 | -4/+3 | |
2021-06-22 | Update development version of online docs | Johannes Ranke | 8 | -9289/+1019 | |
2021-06-17 | Let backtransform_odeparms handle nlmixr formation fractions | Johannes Ranke | 11 | -149/+243 | |
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr | |||||
2021-06-16 | Translate formation fractions to nlmixr language | Johannes Ranke | 4 | -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. | |||||
2021-06-12 | Small cosmetics | Johannes Ranke | 4 | -13/+36 | |
2021-06-11 | Fix package name for travis config... | Johannes Ranke | 1 | -1/+1 | |
2021-06-11 | Fix travis syntax | Johannes Ranke | 1 | -1/+4 | |
2021-06-11 | Add packages necessary for shell commands on travis | Johannes Ranke | 1 | -1/+1 | |
2021-06-11 | Attempt to satisfy nlme version requirement on travis | Johannes Ranke | 1 | -0/+1 | |
2021-06-11 | Add system requirements for symengine on Travis | Johannes Ranke | 1 | -0/+1 | |
nlmixr depends on symengine | |||||
2021-06-11 | Finished 'summary.nlmixr.mmkin', checks, docs | Johannes Ranke | 62 | -571/+15632 | |
2021-06-09 | Rudimentary support for setting up nlmixr models | Johannes Ranke | 20 | -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 | |||||
2021-04-21 | Merge branch 'master' into saemix | Johannes Ranke | 134 | -374/+445 | |
2021-04-21 | Version 1.0.4 published yesterdayv1.0.4 | Johannes Ranke | 26 | -143/+158 | |
2021-03-31 | Bug fix in plot.mkinfit | Johannes Ranke | 128 | -248/+327 | |
In residual plots, use xlab and xlim if appropriate | |||||
2021-03-20 | Fix mkin calculation of saemix residuals | Johannes Ranke | 1 | -1/+1 | |
2021-03-19 | test_log_parms for plot.mixed.mmkin, roxygen run | Johannes Ranke | 6 | -6/+31 | |
2021-03-16 | Convenience option to set nbiter.saemix | Johannes Ranke | 1 | -1/+5 | |
2021-03-09 | Some improvements for borderline cases | Johannes Ranke | 52 | -3926/+4040 | |
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() | |||||
2021-02-24 | Merge branch 'master' into saemix | Johannes Ranke | 2 | -3/+3 | |
2021-02-24 | Clarify version status in NEWS | Johannes Ranke | 3 | -4/+4 | |
2021-02-24 | Merge branch 'master' into saemix | Johannes Ranke | 17 | -12/+36 | |
2021-02-24 | Rebuild docs | Johannes Ranke | 15 | -11/+25 | |
2021-02-24 | Reset graphical parameters with on.exit() | Johannes Ranke | 6 | -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. | |||||
2021-02-24 | Reset graphical parameters with on.exit() | Johannes Ranke | 4 | -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. | |||||
2021-02-18 | Merge branch 'master' into saemix | Johannes Ranke | 13 | -135/+96 | |
2021-02-15 | Don't let pkgdown add release dates | Johannes Ranke | 4 | -99/+57 | |
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated. |