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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-07 12:03:40 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-07 14:55:21 +0100
commit7035cde3a53781721fe15a8893fdf328c789bdd2 (patch)
treea1e4929faf9d645caedc0ed4dcc5036252497c63 /tests/testthat/summary_nlmixr_saem_biphasic.txt
parent77c248ca40b82ec00a756cd82f12968131f78959 (diff)
Remove nlmixr interface for release of mkin 1.1.0
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
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diff --git a/tests/testthat/summary_nlmixr_saem_biphasic.txt b/tests/testthat/summary_nlmixr_saem_biphasic.txt
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@@ -1,97 +0,0 @@
-nlmixr version used for fitting: 2.0.6
-mkin version used for pre-fitting: Dummy 0.0 for testing
-R version used for fitting: Dummy R version for testing
-Date of fit: Dummy date for testing
-Date of summary: Dummy date for testing
-
-Equations:
-d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
- time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
- * parent
-d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
- * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
- exp(-k2 * time))) * parent - k_m1 * m1
-
-Data:
-507 observations of 2 variable(s) grouped in 15 datasets
-
-Degradation model predictions using RxODE
-
-Fitted in test time 0 s
-
-Variance model: Two-component variance function
-
-Mean of starting values for individual parameters:
- parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
- 100.65 -5.38 -0.09 -2.74 -4.53
- g_qlogis
- -0.14
-
-Mean of starting values for error model parameters:
-sigma_low_parent rsd_high_parent sigma_low_m1 rsd_high_m1
- 0.79 0.05 0.79 0.05
-
-Fixed degradation parameter values:
-None
-
-Results:
-
-Likelihood calculated by gauss3_1.6
- AIC BIC logLik
- 2400 2468 -1184
-
-Optimised parameters:
- est. lower upper
-parent_0 100.35 99.0 101.7
-log_k_m1 -5.35 -5.5 -5.2
-f_parent_qlogis -0.09 -0.3 0.1
-log_k1 -2.76 -3.0 -2.6
-log_k2 -4.49 -4.6 -4.4
-g_qlogis -0.17 -0.4 0.1
-
-Correlation:
- pr_0 l__1 f_p_ lg_1 lg_2
-log_k_m1 -0.4
-f_parent_qlogis -0.4 0.4
-log_k1 0.2 -0.2 -0.1
-log_k2 0.0 0.1 0.0 0.3
-g_qlogis 0.1 -0.1 0.0 -0.4 -0.5
-
-Random effects (omega):
- eta.parent_0 eta.log_k_m1 eta.f_parent_qlogis eta.log_k1
-eta.parent_0 0.08 0.00 0.0 0.00
-eta.log_k_m1 0.00 0.02 0.0 0.00
-eta.f_parent_qlogis 0.00 0.00 0.1 0.00
-eta.log_k1 0.00 0.00 0.0 0.09
-eta.log_k2 0.00 0.00 0.0 0.00
-eta.g_qlogis 0.00 0.00 0.0 0.00
- eta.log_k2 eta.g_qlogis
-eta.parent_0 0.00 0.0
-eta.log_k_m1 0.00 0.0
-eta.f_parent_qlogis 0.00 0.0
-eta.log_k1 0.00 0.0
-eta.log_k2 0.03 0.0
-eta.g_qlogis 0.00 0.1
-
-Variance model:
-sigma_low_parent rsd_high_parent sigma_low_m1 rsd_high_m1
- 1.04 0.05 0.82 0.06
-
-Backtransformed parameters:
- est. lower upper
-parent_0 1e+02 1e+02 1e+02
-k_m1 5e-03 4e-03 6e-03
-f_parent_to_m1 5e-01 4e-01 5e-01
-k1 6e-02 5e-02 8e-02
-k2 1e-02 1e-02 1e-02
-g 5e-01 4e-01 5e-01
-
-Resulting formation fractions:
- ff
-parent_m1 0.5
-parent_sink 0.5
-
-Estimated disappearance times:
- DT50 DT90 DT50back DT50_k1 DT50_k2
-parent 25 150 45 11 61
-m1 145 483 NA NA NA

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