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2020-11-11Skip vdiffr tests on travis as they are not robustJohannes Ranke1-1/+2
As can be seen in the miniscule change seen on R-devel in the reference plot updated with this commit
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke1-2/+5
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke2-3/+11
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke3-34/+12
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 Ranke3-103/+41
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke2-6/+96
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 Ranke1-7/+16
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60
2020-11-08Improve saem method, add summaryJohannes Ranke3-8/+108
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke2-57/+42
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 Ranke2-24/+29
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 Ranke1-14/+39
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 Ranke4-53/+47
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix link and update docsJohannes Ranke1-2/+2
2020-11-04Update dynamic docsJohannes Ranke1-4/+7
2020-11-03Do not test residuals per default, improve nlme.mmkinJohannes Ranke1-0/+3
Do not give starting values for random effects in nlme.mmkin.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke4-10/+113
Improve and update docs
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke3-15/+13
2020-10-24Fix a bug for nlme with parent only, improve examplesJohannes Ranke1-29/+8
2020-10-24Improve plot layoutJohannes Ranke1-11/+4
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke3-30/+72
Update docs
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 Ranke3-8/+66
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
2020-10-15Get current nlme version from CRAN on TravisJohannes Ranke1-1/+2
Also commit the dontrun instruction for saemix I had wanted to commit and switch back to devel mode for pkgdown
2020-10-15Updating docs of current dev versionJohannes Ranke1-1/+25
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-0/+54
2020-10-08Fix issues for releaseJohannes Ranke1-54/+0
2020-09-10Regenerate docs with current roxygenJohannes Ranke2-3/+5
2020-07-15Improve testsJohannes Ranke1-2/+3
- 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
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke1-0/+65
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-63/+0
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.
2020-05-27Improve mkinmod docsJohannes Ranke1-26/+39
2020-05-26Use all cores per default, confint toleranceJohannes Ranke5-10/+31
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.
2020-05-25Tell travis where to find the required saemix versionJohannes Ranke1-6/+4
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+43
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-15Improve docsJohannes Ranke1-7/+1
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke1-24/+24
2020-05-14Update version number, better example formattingJohannes Ranke1-1/+4
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-2/+17
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-1/+1
2020-05-12Another documentation updateJohannes Ranke1-11/+8
2020-05-12Update vignettes and docsJohannes Ranke1-1/+1
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke7-7/+7
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke30-225/+236
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+8
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-8/+5
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke4-22/+22
This increases performance up to a factor of five!
2020-05-08Slight performance gain by reducing default n.outtimesJohannes Ranke1-2/+2

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