From 5364f037a72863ef5ba81e14ba4417f68fd389f9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:14:47 +0100 Subject: Make mixed model test data permanent to ensure reproducibility 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. --- tests/testthat/summary_hfit_sfo_tc.txt | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) (limited to 'tests/testthat/summary_hfit_sfo_tc.txt') diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index 41743091..bb5bf6fb 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -8,7 +8,7 @@ Equations: d_parent/dt = - k_parent * parent Data: -106 observations of 1 variable(s) grouped in 6 datasets +104 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical @@ -28,15 +28,15 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 533 531 -261 + 524 523 -257 Optimised parameters: - est. lower upper -parent_0 101.02 99.58 102.46 -log_k_parent -3.32 -3.53 -3.11 -a.1 0.91 0.64 1.17 -b.1 0.05 0.04 0.06 -SD.log_k_parent 0.27 0.11 0.42 + est. lower upper +parent_0 100.68 99.27 102.08 +log_k_parent -3.38 -3.55 -3.21 +a.1 0.87 0.59 1.14 +b.1 0.05 0.04 0.06 +SD.log_k_parent 0.21 0.09 0.33 Correlation: pr_0 @@ -44,18 +44,18 @@ log_k_parent 0.1 Random effects: est. lower upper -SD.log_k_parent 0.3 0.1 0.4 +SD.log_k_parent 0.2 0.09 0.3 Variance model: est. lower upper -a.1 0.91 0.64 1.17 +a.1 0.87 0.59 1.14 b.1 0.05 0.04 0.06 Backtransformed parameters: est. lower upper -parent_0 1e+02 1e+02 1e+02 -k_parent 4e-02 3e-02 4e-02 +parent_0 1e+02 99.27 1e+02 +k_parent 3e-02 0.03 4e-02 Estimated disappearance times: DT50 DT90 -parent 19 64 +parent 20 68 -- cgit v1.2.1 From aaa4cab7e0c7212f91147a9789af54b97fe342ca Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 29 Nov 2022 20:23:17 +0100 Subject: Complete starting values in summary for saem.mmkin fits Also update tests to the changes in mhmkin (see NEWS) --- tests/testthat/summary_hfit_sfo_tc.txt | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'tests/testthat/summary_hfit_sfo_tc.txt') diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index bb5bf6fb..0a61f75f 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -17,13 +17,22 @@ Using 300, 100 iterations and 9 chains Variance model: Two-component variance function -Mean of starting values for individual parameters: +Starting values for degradation parameters: parent_0 log_k_parent 101 -3 Fixed degradation parameter values: None +Starting values for random effects (square root of initial entries in omega): + parent_0 log_k_parent +parent_0 4 0.0 +log_k_parent 0 0.4 + +Starting values for error model parameters: +a.1 b.1 + 1 1 + Results: Likelihood computed by importance sampling -- cgit v1.2.1 From 74e44dfed5af6e6fd421abe82d3e3f190771f85a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Dec 2022 11:20:00 +0100 Subject: Possibility to manually specify no_random_effects in mhmkin --- tests/testthat/summary_hfit_sfo_tc.txt | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) (limited to 'tests/testthat/summary_hfit_sfo_tc.txt') diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index 0a61f75f..0618c715 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -8,7 +8,7 @@ Equations: d_parent/dt = - k_parent * parent Data: -104 observations of 1 variable(s) grouped in 6 datasets +95 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical @@ -19,7 +19,7 @@ Variance model: Two-component variance function Starting values for degradation parameters: parent_0 log_k_parent - 101 -3 + 94 -2 Fixed degradation parameter values: None @@ -27,7 +27,7 @@ None Starting values for random effects (square root of initial entries in omega): parent_0 log_k_parent parent_0 4 0.0 -log_k_parent 0 0.4 +log_k_parent 0 0.7 Starting values for error model parameters: a.1 b.1 @@ -37,15 +37,15 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 524 523 -257 + 542 541 -266 Optimised parameters: - est. lower upper -parent_0 100.68 99.27 102.08 -log_k_parent -3.38 -3.55 -3.21 -a.1 0.87 0.59 1.14 -b.1 0.05 0.04 0.06 -SD.log_k_parent 0.21 0.09 0.33 + est. lower upper +parent_0 92.52 89.11 95.9 +log_k_parent -1.66 -2.07 -1.3 +a.1 2.03 1.60 2.5 +b.1 0.09 0.07 0.1 +SD.log_k_parent 0.51 0.22 0.8 Correlation: pr_0 @@ -53,18 +53,18 @@ log_k_parent 0.1 Random effects: est. lower upper -SD.log_k_parent 0.2 0.09 0.3 +SD.log_k_parent 0.5 0.2 0.8 Variance model: est. lower upper -a.1 0.87 0.59 1.14 -b.1 0.05 0.04 0.06 +a.1 2.03 1.60 2.5 +b.1 0.09 0.07 0.1 Backtransformed parameters: - est. lower upper -parent_0 1e+02 99.27 1e+02 -k_parent 3e-02 0.03 4e-02 + est. lower upper +parent_0 92.5 89.1 95.9 +k_parent 0.2 0.1 0.3 Estimated disappearance times: DT50 DT90 -parent 20 68 +parent 4 12 -- cgit v1.2.1