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2020-12-10Add a test for saemix with deSolveJohannes Ranke3-17/+32
But skip the test as it takes too long to always run
2020-12-09Make saem using mkinpredict work againJohannes Ranke4-67/+78
I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken.
2020-12-09Some test fixesJohannes Ranke4-44/+11
2020-12-09Add more tests and fix HS in saemJohannes Ranke6-1224/+1318
2020-12-09Fix a test I accidentally brokeJohannes Ranke2-18/+13
2020-12-09And moreJohannes Ranke3-1/+16
2020-12-09Any yet more testsJohannes Ranke5-17/+36
2020-12-09Update test output and reduce precision for travisJohannes Ranke4-27/+27
2020-12-09More testsJohannes Ranke10-2613/+1533
2020-12-09Try other mixed fits for vdiffr on travisJohannes Ranke4-4810/+1290
2020-12-09Test print method for mixed.mmkinJohannes Ranke4-4/+34
2020-12-09Make tests more robust, remove two redundant onesJohannes Ranke4-44/+22
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

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