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2022-11-01Improved printing for illparms()Johannes Ranke1-0/+2
For the case of single fits and no ill-defined parameters found
2022-10-31Fix R CMD checkJohannes Ranke1-0/+2
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke1-1/+2
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-28Export status method for mhmkin, move to status.RJohannes Ranke1-0/+1
2022-10-28Rename 'convergence' method to 'status'Johannes Ranke1-8/+7
The reason is that it is misleading in the case of saem.mmkin objects, because convergence is not really checked there.
2022-10-26Remove kernel density estimate from llhistJohannes Ranke1-1/+0
2022-10-25Complete documentation and fix a bugJohannes Ranke1-0/+4
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations.
2022-10-21Add a simple anova method for model comparisonJohannes Ranke1-0/+2
Update docs
2022-10-17SFORB in saem, update for mhmkin and multistartJohannes Ranke1-0/+2
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke1-0/+4
- Add 'best' and 'which.best' generics with methods for multistart objects - Per default, scale the parameters in parhist plots using the fit with the highest log likelihood.
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke1-0/+2
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke1-0/+3
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-1/+7
2022-09-14Remove purrr dependencyJohannes Ranke1-1/+1
We now directly import from rlang and vctrs, which were indirect dependencies anyways. purrr::map_dfr is deprecated in the upcoming purrr 1.0, and depends on dplyr (since when?) which is only suggested by purrr. This would lead new installations of mkin to fail if dplyr is not installed as well.
2022-09-13More work on multistartJohannes Ranke1-0/+3
2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke1-0/+2
2022-08-10Batch processing for hierarchical fitsJohannes Ranke1-0/+13
- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs
2022-07-21Summary method for mmkin objectsJohannes Ranke1-0/+9
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-15/+0
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke1-0/+4
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke1-0/+2
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke1-0/+5
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-0/+8
- 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
2021-02-06Reintroduce interface to saemixJohannes Ranke1-0/+8
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-8/+0
- 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
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-0/+3
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke1-3/+0
With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13
2020-11-20export create_deg_funcJohannes Ranke1-0/+1
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-0/+5
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke1-0/+1
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-2/+1
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 Ranke1-1/+1
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke1-0/+2
2020-11-08Improve saem method, add summaryJohannes Ranke1-0/+3
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke1-2/+2
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.
2020-11-06Make saemix an S3 generic in this packageJohannes Ranke1-3/+2
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 Ranke1-0/+3
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-0/+3
Improve and update docs
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+1
Update docs
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-0/+5
2020-10-08Fix issues for releaseJohannes Ranke1-5/+0
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-1/+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
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-0/+1
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.
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+1
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 Ranke1-0/+2
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-0/+1
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-0/+1
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-0/+2
2020-04-15Include random effects in starting parametersJohannes Ranke1-0/+3
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO

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