Reduced sfo model for multistart.saem.mkin tests

6 files changed, 147 insertions, 45 deletions

diff --git a/log/test.log b/log/test.log
index c5bc0e44..d9dcffb9 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,11 +1,11 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.2s]
+✔ |         5 | Analytical solutions for coupled models [3.3s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [32.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.1s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
@@ -16,7 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.1s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.2s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
@@ -27,31 +27,31 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |         4 | Multistart method for saem.mmkin models [33.5s]
+✔ |         5 | Multistart method for saem.mmkin models [34.8s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
-✔ |        16 | Plotting [9.9s]
+✔ |        16 | Plotting [10.0s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  35 | saemix parent models [71.4s]
+✔ |     1  35 | saemix parent models [65.3s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_saemix_parent.R:143:3): We can also use mkin solution methods for saem
+Skip (test_saemix_parent.R:142:3): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
 ✔ |        11 | Processing of residue series
-✔ |         7 | Fitting the SFORB model [3.8s]
+✔ |         7 | Fitting the SFORB model [3.7s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s]
-✔ |         9 | Hypothesis tests [8.2s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [8.1s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 203.0 s
+Duration: 198.3 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 • This still takes almost 2.5 minutes although we do not solve ODEs (1)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 257 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 258 ]
diff --git a/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg
index 21fa8af8..4342df9b 100644
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+++ b/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg
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diff --git a/tests/testthat/_snaps/multistart/parhist-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/parhist-for-sfo-fit.svg
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+<text x='44.64' y='490.26' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='16.68px' lengthAdjust='spacingAndGlyphs'>0.5</text>
+<text x='44.64' y='284.93' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='16.68px' lengthAdjust='spacingAndGlyphs'>1.0</text>
+<text x='44.64' y='164.82' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='16.68px' lengthAdjust='spacingAndGlyphs'>1.5</text>
+<text x='44.64' y='79.60' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='16.68px' lengthAdjust='spacingAndGlyphs'>2.0</text>
+<text transform='translate(12.96,280.80) rotate(-90)' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='124.73px' lengthAdjust='spacingAndGlyphs'>Normalised parameters</text>
+<polygon points='59.04,502.56 689.76,502.56 689.76,59.04 59.04,59.04 ' style='stroke-width: 0.75; fill: none;' />
+</g>
+<g clip-path='url(#cpNTkuMDR8Njg5Ljc2fDU5LjA0fDUwMi41Ng==)'>
+<circle cx='140.80' cy='280.97' r='8.10' style='stroke-width: 0.75; stroke: #61D04F;' />
+<circle cx='257.60' cy='281.05' r='8.10' style='stroke-width: 0.75; stroke: #61D04F;' />
+<circle cx='140.80' cy='280.75' r='5.40' style='stroke-width: 0.75; stroke: #DF536B;' />
+<circle cx='257.60' cy='280.67' r='5.40' style='stroke-width: 0.75; stroke: #DF536B;' />
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+<circle cx='104.62' cy='437.18' r='2.70' style='stroke-width: 0.75; stroke: #61D04F;' />
+<circle cx='104.62' cy='451.58' r='2.70' style='stroke-width: 0.75; stroke: #DF536B;' />
+<circle cx='104.62' cy='465.98' r='2.70' style='stroke-width: 0.75;' />
+<text x='126.22' y='441.31' style='font-size: 12.00px; font-family: sans;' textLength='105.39px' lengthAdjust='spacingAndGlyphs'>Starting parameters</text>
+<text x='126.22' y='455.71' style='font-size: 12.00px; font-family: sans;' textLength='62.03px' lengthAdjust='spacingAndGlyphs'>Original run</text>
+<text x='126.22' y='470.11' style='font-size: 12.00px; font-family: sans;' textLength='75.36px' lengthAdjust='spacingAndGlyphs'>Multistart runs</text>
+</g>
+</svg>
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 4de2674f..777c998a 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -183,6 +183,7 @@ nlme_biphasic <- suppressWarnings(nlme(mmkin_biphasic))
 
 # saemix
 sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
+sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0")
 dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin",
   no_random_effect = "parent_0")
 
diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R
index 60fdefdc..e5b44e78 100644
--- a/tests/testthat/test_multistart.R
+++ b/tests/testthat/test_multistart.R
@@ -1,10 +1,14 @@
 context("Multistart method for saem.mmkin models")
 
 test_that("multistart works for saem.mmkin models", {
-  saem_sfo_s_multi <- multistart(sfo_saem_1, n = 8, cores = n_cores)
+  set.seed(123456)
+  saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores,
+    no_random_effect = "parent_0")
 
-  llhist_sfo <- function() llhist(saem_sfo_s_multi, xlim = c(-644, -647))
+  llhist_sfo <- function() llhist(saem_sfo_s_multi)
+  parhist_sfo <- function() parhist(saem_sfo_s_multi, ylim = c(0.5, 2))
   vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo)
+  vdiffr::expect_doppelganger("parhist for sfo fit", parhist_sfo)
 
   set.seed(123456)
   saem_biphasic_m_multi <- multistart(saem_biphasic_m, n = 8,
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index d8b6b19e..193dcdcd 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -10,8 +10,7 @@ test_that("Parent fits using saemix are correctly implemented", {
   # We did not introduce variance of parent_0 in the data generation
   # This is correctly detected
   expect_equal(illparms(sfo_saem_1), "sd(parent_0)")
-  # So we remove this variance
-  sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0")
+  # So we have also done a fit without this variance
   expect_equal(illparms(sfo_saem_1_reduced), character(0))
 
   # We cannot currently do the fit with completely fixed initial values