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2020-12-09Fix tests and rerunJohannes Ranke5-111/+98
2020-12-09Some more tests that may work on travis nowJohannes Ranke2-27/+28
2020-12-09Some more testsJohannes Ranke6-69/+196
2020-12-09Don't test on devel, skip failing vdiffr testsJohannes Ranke2-2/+1
I can test on R-devel locally for preparing releases
2020-12-08Test plots on R-release and cache packages againJohannes Ranke24-3138/+3139
2020-12-08Do not cache packagesJohannes Ranke1-2/+0
2020-12-08Install svglite from github on travisJohannes Ranke1-0/+1
2020-12-08Try to figure out while vdiffr failsJohannes Ranke1-4/+4
2020-12-08mixed.mmkin and test coverageJohannes Ranke24-88/+10487
2020-12-07Updates after inline 0.3.17 has been releasedJohannes Ranke2-2/+2
2020-12-07Possibility to use saemix transformations in some casesJohannes Ranke1-45/+127
Namely for SFO, DFOP, SFO-SFO and DFOP-SFO
2020-12-07Attempt to be more failsafe in saemix runsJohannes Ranke1-2/+8
2020-12-03Small doc improvementJohannes Ranke1-2/+2
2020-12-02Possibility to specify random effects structuresJohannes Ranke4-40/+33
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke120-2656/+957
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke9-58/+86
2020-11-27Update static docsJohannes Ranke4-6/+7
2020-11-27Merge branch 'saving_compiled_code'Johannes Ranke7-67/+137
2020-11-27Closes #11Johannes Ranke1-0/+2
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke7-51/+67
Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke8-66/+120
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 Ranke2-0/+2
2020-11-19Update tests, improve CAKE_export testJohannes Ranke4-24/+25
2020-11-19Depend on parallel, doc improvementsJohannes Ranke144-1572/+3637
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-13More work on f_time_norm_focusJohannes Ranke4-11/+22
2020-11-13Fixes for f_time_norm_focus, still very fragile...Johannes Ranke4-18/+49
2020-11-13Annotation of the fixJohannes Ranke1-1/+1
2020-11-13Fixed plotting of non-analytical solutions in saemJohannes Ranke3-22/+26
2020-11-12Model names in lrtest.mmkin, fix for print.mmkinJohannes Ranke2-2/+5
Fix the display of warnings and errors in print.mmkin, the matrix was erroneously transposed.
2020-11-12Update test outputJohannes Ranke1-1/+2
2020-11-12Use preprocessed data for 2,4-D, update docsJohannes Ranke5-40/+44
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke27-41/+585
- 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()
2020-11-11Update static docsJohannes Ranke7-269/+306
2020-11-11Fix example code that was broken by use_of_ff = "max"Johannes Ranke1-6/+10
which is now the default
2020-11-11Fix docs and passing of dot arguments for saemJohannes Ranke1-6/+2
2020-11-11Rename saemix file, option to suppress saemix messagesJohannes Ranke1-4/+10
2020-11-11Skip vdiffr tests on travis as they are not robustJohannes Ranke7-13/+17
As can be seen in the miniscule change seen on R-devel in the reference plot updated with this commit
2020-11-11Check on r-devel, address NOTEJohannes Ranke2-6/+17
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke14-65/+112
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke12-82/+137
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 Ranke25-213/+450
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 Ranke19-359/+694
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke14-15/+637
2020-11-09object$mmkin_orig -> object$mmkinJohannes Ranke3-12/+10
2020-11-09Fix std in summary.nlme.mmkin(..., data = TRUE)Johannes Ranke1-1/+5
2020-11-09Remove outdated doc pageJohannes Ranke1-1202/+0
2020-11-09Doc improvementsJohannes Ranke4-6/+9
2020-11-09Some work on example code, pkgdown updateJohannes Ranke14-212/+451
2020-11-09Custom analytical solutions for saemixJohannes Ranke6-70/+183
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60

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