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2023-08-29Run tests on slimbook: 573.5 sHEADdevJohannes Ranke1-103/+36
Compared with 262.6 s on my main desktop
2023-08-17Update tests without any openblas variantJohannes Ranke2-17/+69
This even a bit faster.
2023-08-17Update test log with libopenblas0-pthreadJohannes Ranke1-49/+15
2023-08-17Update platform specific tests on desktopJohannes Ranke2-34/+83
2023-08-09Update static docsv1.2.5Johannes Ranke1-2/+0
2023-08-09Don't install saemix 3.2 from github any moreRanke Johannes1-17/+17
Emmanuelle has made an official release to CRAN in June
2023-08-08Update docs, check and test on RStudio serverRanke Johannes3-54/+44
2023-08-04Mesotrione data and vignetteJohannes Ranke3-36/+41
The vignette illustrates pH dependent degradation (covariate modelling) with some detail for the parent compound. Also, a bug in the saem method of the illparms function was fixed, which prevented to find ill-defined parameters in cases where e.g. slopes of covariate models have a negative estimate.
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke3-24/+23
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
2023-04-16Skip the Eigenvalue based saem testJohannes Ranke1-8/+12
It took too long, and this solution method is not recommended. We are saving 140 seconds here on my system, so more time is saved on travis.
2023-04-15Increase test coverageJohannes Ranke2-17/+22
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Make predefined symbols saferJohannes Ranke1-14/+15
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows.
2023-04-06Fix a bug with moved DLLs and current deSolveJohannes Ranke2-20/+15
In mkinmod, dll_info was not included in the returned model object in the case that the DLL was moved to a user defined directory. This is now fixed.
2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke2-16/+21
2023-04-01Update tests on 5950xJohannes Ranke2-44/+37
Update platform dependent test plots
2023-03-23Support covariates in endpoints()Johannes Ranke2-24/+24
2023-03-22Fix typo in mkinerrminJohannes Ranke2-34/+41
Thanks to Sebastian Meyer for spotting it.
2023-02-17Update benchmark results for 7950XJohannes Ranke1-1/+1
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke3-39/+20
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-12/+22
2022-12-19Rename template folder, create formatJohannes Ranke1-5/+16
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.
2022-12-15List random effects correlations in output if anyJohannes Ranke1-10/+10
Update docs
2022-12-12Run tests with new CPU and RAMJohannes Ranke1-26/+26
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke1-25/+16
2022-12-06Some parplot improvementsJohannes Ranke1-16/+25
llquant argument, improved legend text, tests
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 error message at testthat terminationJohannes Ranke1-24/+23
https://github.com/r-lib/processx/issues/236
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke2-28/+28
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke2-18/+18
Also update tests to the changes in mhmkin (see NEWS)
2022-11-19Confirm which test fail on R-develv1.2.1Johannes Ranke2-36/+110
2022-11-18Move two saem fits from setup script to skipped testsJohannes Ranke1-22/+22
Save winbuilder/CRAN check time...
2022-11-18Use cluster with two cores to reduce windows check timeJohannes Ranke1-18/+19
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke2-16/+16
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 Ranke2-11/+11
This will hopefully make the test pass on all relevant platforms.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke2-19/+20
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.
2022-11-18Improve logLik.mkinfit to attach nobs attributeJohannes Ranke1-29/+32
The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday.
2022-11-16Reduce testing on CRAN serversv1.2.0Johannes Ranke1-1/+0
2022-11-16Update DESCRIPTION and NEWS, check and testJohannes Ranke2-20/+20
2022-11-16Address platform dependence that surfaced on winbuilderJohannes Ranke1-23/+23
2022-11-15Import saemix for easier profiling, update online docsJohannes Ranke1-8/+8
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke2-18/+18
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-08Show DFOP g equivalent of SFORB in summary, testJohannes Ranke1-13/+13
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke1-13/+13
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke1-20/+20
I do not know why the formulae for b1 and b2 on page 64 of FOCUS kinetics (2014) were not simplified. Clearly, the term k12 * k21 - (k12 + k1output) * k21) can be simplified to - k1output * k21 The test for equivalence of DFOP and SFORB fits verifies that the change is OK. I also removed trailing whitespaces, substituted tab characters by two whitespaces and removed indenting of text in paragraphs describing parameters in roxygen comments to unify formatting.
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke2-21/+21
Based on parameters in the separate fits that fail the t-test.
2022-11-04Never fail with errors in saem.mmkinJohannes Ranke1-8/+2
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-01Add read_spreadsheetJohannes Ranke1-1/+1
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke2-10/+10
2022-11-01Fix illparms testsJohannes Ranke1-45/+12
2022-11-01Improved printing for illparms()Johannes Ranke2-17/+50
For the case of single fits and no ill-defined parameters found

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