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7 daysFix solution type "deSolve" for a special caseHEADdevJohannes Ranke1-0/+19
The special case occurs if not observed data for time zero are available. Fixes #16. Write NEWS and update docs. A lot of html was regenerated, because I had checked out the main branch in between, which made pkgdown believe that I have changed the help files.
7 daysSome test improvementsJohannes Ranke2-1/+15
- Another test for analytical solution of SFO-SFO This is a bit redundant, because we have tests using those solutions in test_analytical.R, where mkinfit is used. But nevertheless, it is good to know that using mkinpredict directly also passes the test. - A more explicit testing of the warning message that is issued if a use turns of transformation of formation fractions
10 daysAxis legend formatting, update vignettesJohannes Ranke1-0/+0
10 daysImprove legend in parplots of multistart objectsJohannes Ranke2-170/+178
10 daysRestrict number of cores for CRAN checksJohannes Ranke1-1/+1
2024-07-28Make sure test work on my desktop, skip more tests on travisJohannes Ranke1-0/+2
2024-04-27Fix bug in R/create_deg_func.RJohannes Ranke4-4/+21
Closes #13
2023-11-23Bump version, fix test from last commit, check and testJohannes Ranke1-1/+1
2023-11-23fix: 'R/illparms.R': An ill-defined random effect is now also found if there ↵Johannes Ranke1-0/+27
is only one random effect in the model. Also add a test for this.
2023-08-17Update tests without any openblas variantJohannes Ranke5-663/+662
This even a bit faster.
2023-08-17Update platform specific tests on desktopJohannes Ranke5-662/+663
2023-08-17Point to the dmta pathway vignette in the dmta testJohannes Ranke1-2/+5
2023-08-04Mesotrione data and vignetteJohannes Ranke5-663/+662
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.
2023-04-16Skip another test on CRAN to save CPU cyclesJohannes Ranke1-0/+2
2023-04-16Skip the Eigenvalue based saem testJohannes Ranke1-5/+6
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 Ranke2-1/+52
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Fix logic in testJohannes Ranke1-1/+1
2023-04-15Fix platform dependence in testJohannes Ranke1-1/+5
2023-04-15Make predefined symbols saferJohannes Ranke2-0/+54
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.
2023-04-15Move preprocessing of DMTA data to the test setupJohannes Ranke2-11/+12
2023-04-01Update tests on 5950xJohannes Ranke4-121/+121
Update platform dependent test plots
2023-03-22Fix typo in mkinerrminJohannes Ranke4-121/+121
Thanks to Sebastian Meyer for spotting it.
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke25-401/+344
2022-12-06Some parplot improvementsJohannes Ranke3-90/+85
llquant argument, improved legend text, tests
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke4-39/+43
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke5-25/+24
Also update tests to the changes in mhmkin (see NEWS)
2022-11-19Confirm which test fail on R-develv1.2.1Johannes Ranke1-1/+2
2022-11-18Move two saem fits from setup script to skipped testsJohannes Ranke5-12/+18
Save winbuilder/CRAN check time...
2022-11-18Use cluster with two cores to reduce windows check timeJohannes Ranke2-8/+16
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke17-245/+160
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 Ranke2-5/+10
This will hopefully make the test pass on all relevant platforms.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke3-4/+8
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 ...
2022-11-18Typo that did not affect test resultsJohannes Ranke1-1/+1
2022-11-16Reduce testing on CRAN serversv1.2.0Johannes Ranke3-5/+7
2022-11-16Address platform dependence that surfaced on winbuilderJohannes Ranke1-1/+6
2022-11-16We get about 25% performance gainJohannes Ranke1-1/+2
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke8-1341/+1343
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 Ranke1-6/+9
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke3-2/+25
Based on parameters in the separate fits that fail the t-test.
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke1-1/+1
2022-11-01Fix illparms testsJohannes Ranke2-4/+4
2022-11-01Improved printing for illparms()Johannes Ranke2-1/+3
For the case of single fits and no ill-defined parameters found
2022-10-29Another attempt to make the test robustJohannes Ranke2-1/+25
As the last update failed on travis. Now we should be more robust, as rounding to one digit works better when parameters are log-transformed (mkin transformations) in the output.
2022-10-29Make test independent of saemix error model parameter patchJohannes Ranke2-4/+3
As mentioned in d44c17da6d62568b
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke5-5/+6
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-28Update test to renamed methodJohannes Ranke1-1/+1
2022-10-26Really test anova output, test covariatesJohannes Ranke2-5/+22
2022-10-26Don't test parhist and llhist on travis, docsJohannes Ranke1-7/+17
2022-10-26Reduced sfo model for multistart.saem.mkin testsJohannes Ranke5-32/+134

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