From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- tests/testthat/summary_saem_biphasic_s.txt | 77 ++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 tests/testthat/summary_saem_biphasic_s.txt (limited to 'tests/testthat/summary_saem_biphasic_s.txt') diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt new file mode 100644 index 00000000..1e0f1ccc --- /dev/null +++ b/tests/testthat/summary_saem_biphasic_s.txt @@ -0,0 +1,77 @@ +saemix version used for fitting: Dummy 0.0 for testing +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: +509 observations of 2 variable(s) grouped in 15 datasets + +Model predictions using solution type analytical + +Fitted in test time 0 s using 300, 100 iterations + +Variance model: Constant variance + +Mean of starting values for individual parameters: + parent_0 k_m1 f_parent_to_m1 k1 k2 + 1.0e+02 4.8e-03 4.8e-01 6.8e-02 1.3e-02 + g + 4.2e-01 + +Fixed degradation parameter values: +None + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 2645 2654 -1310 + +Optimised parameters: + est. lower upper +parent_0 1.0e+02 99.627 1.0e+02 +k_m1 4.8e-03 0.004 5.6e-03 +f_parent_to_m1 4.8e-01 0.437 5.2e-01 +k1 6.5e-02 0.051 8.0e-02 +k2 1.2e-02 0.010 1.4e-02 +g 4.3e-01 0.362 5.0e-01 + +Correlation: + prnt_0 k_m1 f_p__1 k1 k2 +k_m1 -0.156 +f_parent_to_m1 -0.157 0.372 +k1 0.159 0.000 -0.029 +k2 0.074 0.145 0.032 0.332 +g -0.072 -0.142 -0.044 -0.422 -0.570 + +Random effects: + est. lower upper +SD.parent_0 1.14 0.251 2.03 +SD.k_m1 0.14 -0.073 0.35 +SD.f_parent_to_m1 0.29 0.176 0.41 +SD.k1 0.36 0.211 0.52 +SD.k2 0.18 0.089 0.27 +SD.g 0.32 0.098 0.53 + +Variance model: + est. lower upper +a.1 2.7 2.5 2.9 + +Resulting formation fractions: + ff +parent_m1 0.48 +parent_sink 0.52 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +parent 25 145 44 11 58 +m1 145 481 NA NA NA -- cgit v1.2.1 From c73b2f30ec836c949885784ab576e814eb8070a9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 9 Mar 2021 17:35:47 +0100 Subject: Some improvements for borderline cases - fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() --- tests/testthat/summary_saem_biphasic_s.txt | 48 +++++++++++++++--------------- 1 file changed, 24 insertions(+), 24 deletions(-) (limited to 'tests/testthat/summary_saem_biphasic_s.txt') diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt index 1e0f1ccc..8dfae367 100644 --- a/tests/testthat/summary_saem_biphasic_s.txt +++ b/tests/testthat/summary_saem_biphasic_s.txt @@ -13,7 +13,7 @@ d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) exp(-k2 * time))) * parent - k_m1 * m1 Data: -509 observations of 2 variable(s) grouped in 15 datasets +507 observations of 2 variable(s) grouped in 15 datasets Model predictions using solution type analytical @@ -23,9 +23,9 @@ Variance model: Constant variance Mean of starting values for individual parameters: parent_0 k_m1 f_parent_to_m1 k1 k2 - 1.0e+02 4.8e-03 4.8e-01 6.8e-02 1.3e-02 + 1.0e+02 4.6e-03 4.8e-01 6.4e-02 1.1e-02 g - 4.2e-01 + 4.6e-01 Fixed degradation parameter values: None @@ -34,37 +34,37 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2645 2654 -1310 + 2702 2711 -1338 Optimised parameters: est. lower upper -parent_0 1.0e+02 99.627 1.0e+02 -k_m1 4.8e-03 0.004 5.6e-03 -f_parent_to_m1 4.8e-01 0.437 5.2e-01 -k1 6.5e-02 0.051 8.0e-02 -k2 1.2e-02 0.010 1.4e-02 -g 4.3e-01 0.362 5.0e-01 +parent_0 1.0e+02 1.0e+02 1.0e+02 +k_m1 4.7e-03 3.9e-03 5.6e-03 +f_parent_to_m1 4.8e-01 4.3e-01 5.2e-01 +k1 4.8e-02 3.1e-02 6.5e-02 +k2 1.3e-02 8.7e-03 1.7e-02 +g 5.0e-01 4.1e-01 5.8e-01 Correlation: prnt_0 k_m1 f_p__1 k1 k2 -k_m1 -0.156 -f_parent_to_m1 -0.157 0.372 -k1 0.159 0.000 -0.029 -k2 0.074 0.145 0.032 0.332 -g -0.072 -0.142 -0.044 -0.422 -0.570 +k_m1 -0.152 +f_parent_to_m1 -0.143 0.366 +k1 0.097 -0.014 -0.021 +k2 0.022 0.083 0.023 0.101 +g -0.084 -0.144 -0.044 -0.303 -0.364 Random effects: est. lower upper -SD.parent_0 1.14 0.251 2.03 -SD.k_m1 0.14 -0.073 0.35 -SD.f_parent_to_m1 0.29 0.176 0.41 -SD.k1 0.36 0.211 0.52 -SD.k2 0.18 0.089 0.27 -SD.g 0.32 0.098 0.53 +SD.parent_0 1.22 0.316 2.12 +SD.k_m1 0.15 -0.079 0.38 +SD.f_parent_to_m1 0.32 0.191 0.44 +SD.k1 0.66 0.416 0.90 +SD.k2 0.59 0.368 0.80 +SD.g 0.16 -0.373 0.70 Variance model: est. lower upper -a.1 2.7 2.5 2.9 +a.1 2.9 2.7 3 Resulting formation fractions: ff @@ -73,5 +73,5 @@ parent_sink 0.52 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 25 145 44 11 58 -m1 145 481 NA NA NA +parent 26 127 38 14 54 +m1 146 485 NA NA NA -- cgit v1.2.1 From d75378911cef79b3ed95daef71bf67db413d2ac8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 17 Nov 2021 12:59:49 +0100 Subject: Update required saemix version, update tests --- tests/testthat/summary_saem_biphasic_s.txt | 38 +++++++++++++++--------------- 1 file changed, 19 insertions(+), 19 deletions(-) (limited to 'tests/testthat/summary_saem_biphasic_s.txt') diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt index 8dfae367..bab4bf98 100644 --- a/tests/testthat/summary_saem_biphasic_s.txt +++ b/tests/testthat/summary_saem_biphasic_s.txt @@ -34,33 +34,33 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2702 2711 -1338 + 2679 2689 -1327 Optimised parameters: est. lower upper parent_0 1.0e+02 1.0e+02 1.0e+02 -k_m1 4.7e-03 3.9e-03 5.6e-03 +k_m1 4.8e-03 4.1e-03 5.5e-03 f_parent_to_m1 4.8e-01 4.3e-01 5.2e-01 -k1 4.8e-02 3.1e-02 6.5e-02 -k2 1.3e-02 8.7e-03 1.7e-02 -g 5.0e-01 4.1e-01 5.8e-01 +k1 5.9e-02 4.6e-02 7.2e-02 +k2 1.1e-02 9.0e-03 1.3e-02 +g 4.9e-01 4.3e-01 5.4e-01 Correlation: prnt_0 k_m1 f_p__1 k1 k2 -k_m1 -0.152 -f_parent_to_m1 -0.143 0.366 -k1 0.097 -0.014 -0.021 -k2 0.022 0.083 0.023 0.101 -g -0.084 -0.144 -0.044 -0.303 -0.364 +k_m1 -0.168 +f_parent_to_m1 -0.141 0.379 +k1 0.139 -0.004 -0.024 +k2 0.055 0.154 0.033 0.246 +g -0.078 -0.206 -0.058 -0.435 -0.601 Random effects: - est. lower upper -SD.parent_0 1.22 0.316 2.12 -SD.k_m1 0.15 -0.079 0.38 -SD.f_parent_to_m1 0.32 0.191 0.44 -SD.k1 0.66 0.416 0.90 -SD.k2 0.59 0.368 0.80 -SD.g 0.16 -0.373 0.70 + est. lower upper +SD.parent_0 1.1986 0.28 2.12 +SD.k_m1 0.0034 -6.85 6.86 +SD.f_parent_to_m1 0.3369 0.21 0.46 +SD.k1 0.3790 0.24 0.52 +SD.k2 0.2666 0.16 0.37 +SD.g 0.0401 -0.67 0.75 Variance model: est. lower upper @@ -73,5 +73,5 @@ parent_sink 0.52 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 26 127 38 14 54 -m1 146 485 NA NA NA +parent 25 150 45 12 64 +m1 145 483 NA NA NA -- cgit v1.2.1