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2023-02-17Finish adapting to upcoming deSolveJohannes Ranke18-229/+267
2023-02-17Commit prebuilt vignettes from desktopJohannes Ranke3-0/+0
2023-02-17Merge remote-tracking branch 'origin/main' into faster_lsodaJohannes Ranke4-6/+7
2023-02-17Fix path, build target for prebuilt pdf vignettesJohannes Ranke2-1/+4
2023-02-13Update mmkin docs, parallel is not loaded any moreJohannes Ranke1-4/+3
2023-02-13Prepare to keep prebuilt vignettes as pdf in gitJohannes Ranke1-1/+0
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke5-100/+104
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke494-14040/+33507
2023-01-28Update saem benchmark with new CPUJohannes Ranke3-22/+123
2023-01-28Some improvements to the READMEJohannes Ranke4-53/+202
2023-01-28Build online HTML versions of prebuilt vignettesJohannes Ranke39-49/+10017
Also, give some structure to the menu for selecting articles
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke74-607/+6255
2023-01-05Don't preschedule multistart runsJohannes Ranke1-2/+5
Sometimes a lot of them fail, so we were wasting time
2023-01-04Update documentation of 'use_of_ff' argumentJohannes Ranke1-1/+1
2023-01-03Neutral names for code chunks in the templateJohannes Ranke1-5/+4
2023-01-03Reflect changed name of dll directory in templateJohannes Ranke2-1/+2
2023-01-03Improve template text, use neutral name for dll_dirJohannes Ranke1-6/+6
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke4-22/+175
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2023-01-02Fix no_random_effect with character vectorJohannes Ranke1-1/+1
2023-01-02Echo R code per default in markdown templateJohannes Ranke1-1/+1
2022-12-22Improve code formatting in template skeletonJohannes Ranke1-1/+3
2022-12-19Rename template folder, create formatJohannes Ranke12-48/+110
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-19Template and spreadsheet for hierarchical kineticsJohannes Ranke6-1/+198
The template only shows parent data evaluation without covariate models for now. The spreadsheet will also be useful for unit testing of the read_spreadsheet function.
2022-12-15List random effects correlations in output if anyJohannes Ranke14-274/+422
Update docs
2022-12-12Run tests with new CPU and RAMJohannes Ranke1-26/+26
2022-12-07Fix parplot for the case of failed multistart runsJohannes Ranke3-2/+4
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke4-27/+43
2022-12-06Some parplot improvementsJohannes Ranke9-178/+183
llquant argument, improved legend text, tests
2022-12-02Update online docsJohannes Ranke2-2/+2
2022-12-02Update test log with current R-develJohannes Ranke1-42/+23
One printout and four plots are different using current R-devel. These are currently skipped on CRAN. These test were run with the development version of saemix (my branch installable_dev_version). If saemix from CRAN is used, there are some more differences due to different error model parameters
2022-12-02Avoid redundant warnings in summariesJohannes Ranke2-3/+4
2022-12-02Avoid error message at testthat terminationJohannes Ranke2-26/+29
https://github.com/r-lib/processx/issues/236
2022-12-02Update online docsJohannes Ranke7-14/+95
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke9-94/+187
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke9-45/+55
Also update tests to the changes in mhmkin (see NEWS)
2022-11-25mhmkin: Easy specification of ill-defined parmsJohannes Ranke3-28/+28
The argument 'no_random_effect' now accepts an illparms.mhmkin object
2022-11-24Start online docs of the development versionJohannes Ranke181-8344/+7033
2022-11-22Update and improve READMEJohannes Ranke2-31/+34
2022-11-22Start new development versionJohannes Ranke5-19/+18
2022-11-19Confirm which test fail on R-develv1.2.1Johannes Ranke3-37/+112
2022-11-18Move two saem fits from setup script to skipped testsJohannes Ranke6-34/+40
Save winbuilder/CRAN check time...
2022-11-18Use cluster with two cores to reduce windows check timeJohannes Ranke6-28/+40
2022-11-18Update docsJohannes Ranke14-18/+279
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke24-262/+324
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package.
2022-11-18Round parameters with signif() before printingJohannes Ranke5-17/+24
This will hopefully make the test pass on all relevant platforms.
2022-11-18Prepare follow-up release to fix CRAN checksJohannes Ranke1-2/+2
2022-11-18Remove candidate patches that were accidentally committedJohannes Ranke2-1703/+0
2022-11-18Update NEWSJohannes Ranke1-0/+10
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke9-29/+51
Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart.
2022-11-18Avoid ill-determined fit, it is platform dependentJohannes Ranke2-12/+11
The previous test lead to an error on the Fedora test systems (gcc and clang) on CRAN: ... Results have changed from known value recorded in 'print_dfop_saemix_1.txt'. old[13:24] vs new[13:24] "" "Fitted parameters:" " estimate lower upper" - "parent_0 100.09 98.94 101.25" + "parent_0 100.17 99.01 101.33" - "log_k1 -2.68 -2.91 -2.45" + "log_k1 -2.66 -2.89 -2.43" "log_k2 -4.12 -4.24 -4.00" - "g_qlogis -0.41 -0.63 -0.20" + "g_qlogis -0.43 -0.65 -0.21" - "a.1 0.91 0.67 1.15" + "a.1 0.91 0.67 1.16" "b.1 0.05 0.04 0.06" - "SD.log_k1 0.36 0.21 0.50" + "SD.log_k1 0.35 0.21 0.50" and 2 more ...

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