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2020-11-09I do not have a parms.nlme.mmkin methodJohannes Ranke1-2/+1
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke3-113/+57
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Merge plot methods for nlme.mmkin and saem.mmkinJohannes Ranke3-232/+95
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke1-0/+218
2020-11-09object$mmkin_orig -> object$mmkinJohannes Ranke3-12/+10
2020-11-09Fix std in summary.nlme.mmkin(..., data = TRUE)Johannes Ranke1-1/+5
2020-11-09Doc improvementsJohannes Ranke1-0/+1
2020-11-09Some work on example code, pkgdown updateJohannes Ranke2-17/+31
2020-11-09Custom analytical solutions for saemixJohannes Ranke2-40/+108
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60
2020-11-08The call to saemix.predict fails with DFOP-SFOJohannes Ranke1-3/+3
2020-11-08Improve saem method, add summaryJohannes Ranke5-70/+341
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke2-47/+48
The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm.
2020-11-07Make deSolve predictions within saemix robustJohannes Ranke2-15/+34
Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic
2020-11-06Make saemix an S3 generic in this packageJohannes Ranke1-42/+72
This commit also defined saemix.mmkin for mmkin row objects. This works fine, but if we set the class of the returned object to c("saemix.mmkin", "saemix"), it is not an S4 class any more which make it impossible to use saemix functions on it.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke5-111/+215
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix mean_degparms() if only one optimised parameterJohannes Ranke1-5/+7
2020-11-05Fix link and update docsJohannes Ranke1-2/+2
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke1-1/+1
2020-11-04Update dynamic docsJohannes Ranke1-5/+6
2020-11-04Deprecate cores > 1 in saemix_modelJohannes Ranke1-3/+5
2020-11-03Do not test residuals per default, improve nlme.mmkinJohannes Ranke2-7/+11
Do not give starting values for random effects in nlme.mmkin.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke4-21/+285
Improve and update docs
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke3-20/+34
2020-10-26Fix another bug in plot.nlme.mmkinJohannes Ranke1-1/+2
2020-10-26Fix a bug in plot.nlme.mmkinJohannes Ranke1-1/+3
2020-10-24Fix a bug for nlme with parent only, improve examplesJohannes Ranke2-32/+10
2020-10-24Improve plot layoutJohannes Ranke1-33/+13
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke3-83/+196
Update docs
2020-10-24Printing method for mmkin objectsJohannes Ranke2-8/+51
2020-10-22Really fix check for nlme::varConstPropJohannes Ranke1-1/+2
And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent().
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke3-11/+86
The experimental nlme version in my drat repository contains the variance function structure varConstProp which makes it possible to use the two-component error model in generalized nonlinear models using nlme::gnls() and in mixed effects models using nlme::nlme().
2020-10-15More gentle example for saemix with combined error modelJohannes Ranke1-1/+2
2020-10-15Don't run saemix examples on travis for nowJohannes Ranke1-1/+2
2020-10-15Updating docs of current dev versionJohannes Ranke1-1/+41
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-0/+134
2020-10-08Fix issues for releaseJohannes Ranke1-12/+12
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke1-134/+0
2020-09-01Merge branch 'master' of kolab.jrwb.de:mkinJohannes Ranke1-29/+0
2020-09-01Back-calculated DT50 values for biphasic modelsJohannes Ranke1-1/+10
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-29/+0
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-1/+2
2020-07-15Improve testsJohannes Ranke1-1/+1
- Reduce significant digits for the objective function output in mkinfit(..., quiet = FALSE) as R and R-devel gave different output on my system - Add makefile target 'devtest' for testing with R-devel, in order to fix problems showing up with R-devel on Travis
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke2-22/+29
2020-07-15Use try() within mmkinJohannes Ranke1-1/+1
This keeps mmkin from stopping if one of the fits fails. Instead, a try-error is assigned to the respective position in the mmkin object.
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke2-83/+1
Vignette FOCUS_L failed as I had introduced a bug in the handling of warnings. Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now, see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke3-14/+111
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke2-46/+59
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-1/+1
2020-05-27Improve mkinmod docsJohannes Ranke1-26/+39
2020-05-26Use all cores per default, confint toleranceJohannes Ranke5-50/+78
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.

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