From 448e47e756c0c67fc658f93575092973aa455fb1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 08:53:15 +0200 Subject: Point to the dmta pathway vignette in the dmta test --- tests/testthat/test_dmta.R | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'tests') diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R index cd6de341..3941cae1 100644 --- a/tests/testthat/test_dmta.R +++ b/tests/testthat/test_dmta.R @@ -85,9 +85,12 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid "Iteration 5, LME step.*not converge") ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed") - skip("Fitting this ODE model with saemix takes about 15 minutes on my system") + skip("Fitting this ODE model with saemix takes about 5 minutes on my new system") + # August 2023: Please refer to the mkin vignette for the currently + # recommended way to fit the DMTA pathway data with saemix + # As DFOP is overparameterised and leads to instabilities and errors, we - # need to use SFO. + # need to use SFO with nlme # saem_saemix_sfo_sfo3p_tc <- saem(dmta_sfo_sfo3p_tc) # The fit above, using SFO for the parent leads to low values of DMTA_0 # (confidence interval from 84.4 to 92.8) which is not consistent with what -- cgit v1.2.1 From 9901675e499226eec6304113eb5ffa3b900942c2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:03:53 +0200 Subject: Update platform specific tests on desktop --- .../_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 43 +- ...t-for-saem-object-with-mkin-transformations.svg | 1086 ++++++++++---------- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 166 +-- .../plot/mixed-model-fit-for-nlme-object.svg | 20 +- tests/testthat/print_dfop_saem_1.txt | 10 +- 5 files changed, 663 insertions(+), 662 deletions(-) (limited to 'tests') diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg index 3b9d51fb..6015aed8 100644 --- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg @@ -21,26 +21,28 @@ Frequency of log likelihoods - - - - - + + + + --1149.30 --1149.25 --1149.20 --1149.15 --1149.10 --1149.05 --1149.00 +-1149.5 +-1149.4 +-1149.3 +-1149.2 +-1149.1 +-1149.0 + + 0 -1 -2 +1 +2 +3 +4 @@ -48,13 +50,12 @@ - - - - - - - + + + + + + original fit diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg index 5e534dd1..69fa6a4d 100644 --- a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -249,7 +249,7 @@ - + @@ -342,7 +342,7 @@ - + @@ -856,38 +856,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -933,51 +933,51 @@ - - - + + + - - + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -1502,7 +1502,7 @@ - + @@ -1585,7 +1585,7 @@ - + @@ -1940,17 +1940,17 @@ - + - - - - + + + + 0 -10 -20 -30 -40 +10 +20 +30 +40 @@ -1983,290 +1983,290 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2274,47 +2274,47 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2323,174 +2323,174 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg index ed9168fb..b01dac74 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -25,104 +25,104 @@ - - - + + + - + - - - - - + + + + + - - - - - - + + + + + + - - - + + + - - - - - - + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - + + + + - + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + - - - - - - + + + + + + - - + + - - - - - - - - - + + + + + + + + + - - + + diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg index c94012ce..76fed0dc 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg @@ -813,7 +813,7 @@ - + @@ -833,7 +833,7 @@ - + @@ -900,7 +900,7 @@ - + @@ -921,7 +921,7 @@ - + @@ -964,8 +964,8 @@ - - + + @@ -1243,8 +1243,8 @@ - - + + @@ -1291,8 +1291,8 @@ - - + + diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt index f7354320..bdc40065 100644 --- a/tests/testthat/print_dfop_saem_1.txt +++ b/tests/testthat/print_dfop_saem_1.txt @@ -13,11 +13,11 @@ Likelihood computed by importance sampling Fitted parameters: estimate lower upper -parent_0 99.96 98.82 101.11 -log_k1 -2.71 -2.94 -2.49 -log_k2 -4.14 -4.26 -4.01 -g_qlogis -0.36 -0.54 -0.17 -a.1 0.93 0.69 1.17 +parent_0 99.92 98.77 101.06 +log_k1 -2.72 -2.95 -2.50 +log_k2 -4.14 -4.27 -4.01 +g_qlogis -0.35 -0.53 -0.16 +a.1 0.92 0.68 1.16 b.1 0.05 0.04 0.06 SD.log_k1 0.37 0.23 0.51 SD.log_k2 0.23 0.14 0.31 -- cgit v1.2.1 From bbed90f6a4010ac0b911ec13c04ae06eebc74bb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:23:27 +0200 Subject: Update tests without any openblas variant This even a bit faster. --- .../_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 43 +- ...t-for-saem-object-with-mkin-transformations.svg | 1086 ++++++++++---------- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 166 +-- .../plot/mixed-model-fit-for-nlme-object.svg | 20 +- tests/testthat/print_dfop_saem_1.txt | 10 +- 5 files changed, 662 insertions(+), 663 deletions(-) (limited to 'tests') diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg index 6015aed8..3b9d51fb 100644 --- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg @@ -21,28 +21,26 @@ Frequency of log likelihoods - - - - + + + + + --1149.5 --1149.4 --1149.3 --1149.2 --1149.1 --1149.0 +-1149.30 +-1149.25 +-1149.20 +-1149.15 +-1149.10 +-1149.05 +-1149.00 - - 0 -1 -2 -3 -4 +1 +2 @@ -50,12 +48,13 @@ - - - - - - + + + + + + + original fit diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg index 69fa6a4d..5e534dd1 100644 --- a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -249,7 +249,7 @@ - + @@ -342,7 +342,7 @@ - + @@ -856,38 +856,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -933,51 +933,51 @@ - - - + + + - - + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -1502,7 +1502,7 @@ - + @@ -1585,7 +1585,7 @@ - + @@ -1940,17 +1940,17 @@ - + - - - - + + + + 0 -10 -20 -30 -40 +10 +20 +30 +40 @@ -1983,290 +1983,290 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2274,47 +2274,47 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2323,174 +2323,174 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg index b01dac74..ed9168fb 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -25,104 +25,104 @@ - - - + + + - + - - - - - + + + + + - - - - - - + + + + + + - - - + + + - - - - - - + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - + + + + - + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + - - - - - - + + + + + + - - + + - - - - - - - - - + + + + + + + + + - - + + diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg index 76fed0dc..c94012ce 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg @@ -813,7 +813,7 @@ - + @@ -833,7 +833,7 @@ - + @@ -900,7 +900,7 @@ - + @@ -921,7 +921,7 @@ - + @@ -964,8 +964,8 @@ - - + + @@ -1243,8 +1243,8 @@ - - + + @@ -1291,8 +1291,8 @@ - - + + diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt index bdc40065..f7354320 100644 --- a/tests/testthat/print_dfop_saem_1.txt +++ b/tests/testthat/print_dfop_saem_1.txt @@ -13,11 +13,11 @@ Likelihood computed by importance sampling Fitted parameters: estimate lower upper -parent_0 99.92 98.77 101.06 -log_k1 -2.72 -2.95 -2.50 -log_k2 -4.14 -4.27 -4.01 -g_qlogis -0.35 -0.53 -0.16 -a.1 0.92 0.68 1.16 +parent_0 99.96 98.82 101.11 +log_k1 -2.71 -2.94 -2.49 +log_k2 -4.14 -4.26 -4.01 +g_qlogis -0.36 -0.54 -0.17 +a.1 0.93 0.69 1.17 b.1 0.05 0.04 0.06 SD.log_k1 0.37 0.23 0.51 SD.log_k2 0.23 0.14 0.31 -- cgit v1.2.1