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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
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-0/+2
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke1-0/+2
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-1/+3
2020-04-03Merge branch 'master' into mxkinJohannes Ranke1-0/+1
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-0/+3
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+3
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-0/+1
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+5
- Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat
2019-11-04Scaled residual plotsJohannes Ranke1-0/+1
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-0/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-0/+7
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-26Fix checks and testsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown
2019-10-26parms and confint methodsJohannes Ranke1-0/+3
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-34/+72
2019-04-04Direct error model fitting worksJohannes Ranke1-3/+1
- No IRLS required - Removed optimization algorithms other than Port - Removed the dependency on FME - Fitting the error model 'obs' is much faster for the FOCUS_2006_D dataset and the FOMC_SFO model (1 second versus 3.4 seconds) - Vignettes build slower. Compiled models needs 3 minutes instead of 1.5 - For other vignettes, the trend is less clear. Some fits are faster, even for error_model = "const". FOCUS_Z is faster (34.9 s versus 44.1 s) - Standard errors and confidence intervals are slightly smaller - Removed code for plotting during the fit, as I hardly ever used it - Merged the two cost functions (using transformed and untransformed parameters) into one log-likelihood function
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-4/+12
2019-01-31Restore NAMESPACEJohannes Ranke1-4/+28
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke1-28/+4
2019-01-31Export to CAKE study fileJohannes Ranke1-0/+1
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown

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