aboutsummaryrefslogtreecommitdiff
path: root/tests/testthat
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2019-04-24 21:03:43 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-04-24 21:19:52 +0200
commit380a29e81f88cd80c9c6915200ddc7054c8a085a (patch)
tree93816c95c6bc1604a6edd24ce2617dba54a44fb3 /tests/testthat
parent129ff33d91bbea9a90b11f8230b78493eba45fe3 (diff)
Improve output and update tests
Remove skipped tests as I do not intend to reactivate them
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/DFOP_FOCUS_C_messages.txt90
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt6
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R19
-rw-r--r--tests/testthat/test_logistic.R10
5 files changed, 49 insertions, 78 deletions
diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index 5327b3f6..9abde683 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -1,148 +1,148 @@
parent_0 log_k1 log_k2 g_ilr sigma
85.1 -2.302585 -4.60517 0
-Negative log-likelihood at call 1: 7391.39
+Sum of squared residuals at call 1: 7391.39
85.1 -2.302585 -4.60517 0
85.1 -2.302585 -4.60517 0
-Negative log-likelihood at call 3: 7391.389
+Sum of squared residuals at call 3: 7391.389
85.1 -2.302585 -4.60517 0
-Negative log-likelihood at call 4: 7391.389
+Sum of squared residuals at call 4: 7391.389
85.1 -2.302585 -4.60517 1.490116e-08
85.06371 -1.77328 -4.250366 0.7698268
-Negative log-likelihood at call 6: 2000.127
+Sum of squared residuals at call 6: 2000.127
85.06375 -1.77328 -4.250366 0.7698268
85.06371 -1.773322 -4.250366 0.7698268
85.06371 -1.77328 -4.250408 0.7698268
85.06371 -1.77328 -4.250366 0.7697847
85.03542 -0.9608523 -4.11546 1.336361
-Negative log-likelihood at call 11: 32.97798
+Sum of squared residuals at call 11: 32.97798
85.03542 -0.9608523 -4.11546 1.336361
85.03542 -0.9608526 -4.11546 1.336361
85.03542 -0.9608523 -4.11546 1.336361
85.03542 -0.9608523 -4.11546 1.336361
85.03704 -0.256064 -4.273512 0.6447755
85.03285 -0.7822828 -4.127513 1.312494
-Negative log-likelihood at call 17: 5.348133
+Sum of squared residuals at call 17: 5.348133
85.03286 -0.7822828 -4.127513 1.312494
-Negative log-likelihood at call 18: 5.348132
+Sum of squared residuals at call 18: 5.348132
85.03285 -0.7822828 -4.127513 1.312494
-Negative log-likelihood at call 19: 5.348131
+Sum of squared residuals at call 19: 5.348131
85.03285 -0.7822828 -4.127513 1.312494
85.03285 -0.7822828 -4.127513 1.312494
-Negative log-likelihood at call 21: 5.348131
+Sum of squared residuals at call 21: 5.348131
85.02325 -0.74968 -4.059 1.14891
85.03127 -0.7909068 -4.114802 1.268157
-Negative log-likelihood at call 23: 4.704445
+Sum of squared residuals at call 23: 4.704445
85.03127 -0.7909068 -4.114802 1.268157
-Negative log-likelihood at call 24: 4.704444
+Sum of squared residuals at call 24: 4.704444
85.03127 -0.7909068 -4.114802 1.268157
85.03127 -0.7909068 -4.1148 1.268157
-Negative log-likelihood at call 26: 4.704433
+Sum of squared residuals at call 26: 4.704433
85.03127 -0.7909068 -4.114802 1.268158
85.03001 -0.7801506 -4.069435 1.262797
-Negative log-likelihood at call 28: 4.421625
+Sum of squared residuals at call 28: 4.421625
85.03001 -0.7801506 -4.069435 1.262797
85.03001 -0.7801507 -4.069435 1.262797
-Negative log-likelihood at call 30: 4.421624
+Sum of squared residuals at call 30: 4.421624
85.03001 -0.7801506 -4.069435 1.262797
85.03001 -0.7801506 -4.069435 1.262797
85.02878 -0.7900844 -4.023945 1.256918
85.02964 -0.7857352 -4.054587 1.260236
-Negative log-likelihood at call 34: 4.414346
+Sum of squared residuals at call 34: 4.414346
85.02964 -0.7857352 -4.054587 1.260236
85.02964 -0.7857351 -4.054587 1.260236
-Negative log-likelihood at call 36: 4.414346
+Sum of squared residuals at call 36: 4.414346
85.02964 -0.7857352 -4.054588 1.260236
85.02964 -0.7857352 -4.054587 1.260236
85.02812 -0.7778128 -4.042219 1.25389
-Negative log-likelihood at call 39: 4.372463
+Sum of squared residuals at call 39: 4.372463
85.02812 -0.7778128 -4.042219 1.25389
85.02812 -0.7778129 -4.042219 1.25389
-Negative log-likelihood at call 41: 4.372462
+Sum of squared residuals at call 41: 4.372462
85.02812 -0.7778128 -4.042219 1.25389
85.02812 -0.7778128 -4.042219 1.25389
85.02419 -0.7765144 -4.02942 1.245094
85.0263 -0.7778419 -4.036021 1.249634
-Negative log-likelihood at call 45: 4.369313
+Sum of squared residuals at call 45: 4.369313
85.0263 -0.7778419 -4.036021 1.249634
85.0263 -0.7778418 -4.036021 1.249634
-Negative log-likelihood at call 47: 4.369313
+Sum of squared residuals at call 47: 4.369313
85.0263 -0.7778419 -4.036022 1.249634
85.0263 -0.7778419 -4.036021 1.249634
-Negative log-likelihood at call 49: 4.369313
+Sum of squared residuals at call 49: 4.369313
85.02267 -0.7786811 -4.02967 1.252015
-Negative log-likelihood at call 50: 4.365062
+Sum of squared residuals at call 50: 4.365062
85.02268 -0.7786811 -4.02967 1.252015
85.02267 -0.7786812 -4.02967 1.252015
85.02267 -0.7786811 -4.02967 1.252015
-Negative log-likelihood at call 53: 4.365062
+Sum of squared residuals at call 53: 4.365062
85.02267 -0.7786811 -4.02967 1.252015
85.01633 -0.7763163 -4.027611 1.248897
-Negative log-likelihood at call 55: 4.364078
+Sum of squared residuals at call 55: 4.364078
85.01633 -0.7763163 -4.027611 1.248897
-Negative log-likelihood at call 56: 4.364078
+Sum of squared residuals at call 56: 4.364078
85.01633 -0.7763164 -4.027611 1.248897
-Negative log-likelihood at call 57: 4.364077
+Sum of squared residuals at call 57: 4.364077
85.01633 -0.7763163 -4.027611 1.248897
85.01633 -0.7763163 -4.027611 1.248897
85.00894 -0.7777917 -4.026307 1.24772
-Negative log-likelihood at call 60: 4.364052
+Sum of squared residuals at call 60: 4.364052
85.00894 -0.7777917 -4.026307 1.24772
-Negative log-likelihood at call 61: 4.364052
+Sum of squared residuals at call 61: 4.364052
85.00894 -0.7777917 -4.026307 1.24772
-Negative log-likelihood at call 62: 4.364052
+Sum of squared residuals at call 62: 4.364052
85.00894 -0.7777917 -4.026307 1.24772
85.00894 -0.7777917 -4.026307 1.24772
-Negative log-likelihood at call 64: 4.364052
+Sum of squared residuals at call 64: 4.364052
85.00518 -0.7773082 -4.026004 1.248453
-Negative log-likelihood at call 65: 4.362751
+Sum of squared residuals at call 65: 4.362751
85.00519 -0.7773082 -4.026004 1.248453
85.00518 -0.7773083 -4.026004 1.248453
-Negative log-likelihood at call 67: 4.362751
+Sum of squared residuals at call 67: 4.362751
85.00518 -0.7773082 -4.026005 1.248453
85.00518 -0.7773082 -4.026004 1.248453
85.00134 -0.7776046 -4.025878 1.248775
-Negative log-likelihood at call 70: 4.362721
+Sum of squared residuals at call 70: 4.362721
85.00135 -0.7776046 -4.025878 1.248775
-Negative log-likelihood at call 71: 4.362721
+Sum of squared residuals at call 71: 4.362721
85.00134 -0.7776046 -4.025878 1.248775
-Negative log-likelihood at call 72: 4.362721
+Sum of squared residuals at call 72: 4.362721
85.00134 -0.7776046 -4.025878 1.248775
85.00134 -0.7776046 -4.025878 1.248775
85.0032 -0.7774734 -4.0257 1.248643
-Negative log-likelihood at call 75: 4.362715
+Sum of squared residuals at call 75: 4.362715
85.0032 -0.7774734 -4.0257 1.248643
85.0032 -0.7774734 -4.0257 1.248643
-Negative log-likelihood at call 77: 4.362715
+Sum of squared residuals at call 77: 4.362715
85.0032 -0.7774735 -4.0257 1.248643
85.0032 -0.7774734 -4.0257 1.248643
85.0032 -0.7774734 -4.0257 1.248643
85.0032 -0.7774734 -4.0257 1.248643
85.00249 -0.7774909 -4.025911 1.248679
-Negative log-likelihood at call 82: 4.362715
+Sum of squared residuals at call 82: 4.362715
85.0025 -0.7774909 -4.025911 1.248679
-Negative log-likelihood at call 83: 4.362715
+Sum of squared residuals at call 83: 4.362715
85.00249 -0.7774909 -4.025911 1.248679
85.00249 -0.7774905 -4.025911 1.248679
85.00249 -0.7774914 -4.025911 1.248679
-Negative log-likelihood at call 86: 4.362715
+Sum of squared residuals at call 86: 4.362715
85.00249 -0.7774909 -4.025911 1.248679
85.00249 -0.7774909 -4.025911 1.248679
85.00249 -0.7774909 -4.025911 1.248679
85.00249 -0.7774909 -4.025911 1.248679
85.00274 -0.7774922 -4.025821 1.248672
-Negative log-likelihood at call 91: 4.362714
+Sum of squared residuals at call 91: 4.362714
85.00274 -0.7774922 -4.025821 1.248672
85.00274 -0.7774922 -4.025821 1.248672
-Negative log-likelihood at call 93: 4.362714
+Sum of squared residuals at call 93: 4.362714
85.00274 -0.7774921 -4.025821 1.248672
-Negative log-likelihood at call 94: 4.362714
+Sum of squared residuals at call 94: 4.362714
85.00274 -0.7774922 -4.025821 1.248672
85.00274 -0.7774922 -4.025821 1.248672
85.00274 -0.7774922 -4.025821 1.248672
85.00274 -0.7774922 -4.025821 1.248672
85.00274 -0.7774922 -4.025821 1.248672
85.00273 -0.7774912 -4.025817 1.24867
-Negative log-likelihood at call 100: 4.362714
+Sum of squared residuals at call 100: 4.362714
85.00275 -0.7774912 -4.025817 1.24867
85.00271 -0.7774912 -4.025817 1.24867
85.00273 -0.7774905 -4.025817 1.24867
@@ -152,7 +152,7 @@ Negative log-likelihood at call 100: 4.362714
85.00273 -0.7774912 -4.025817 1.248671
85.00273 -0.7774912 -4.025817 1.248669
85.00274 -0.7774913 -4.025819 1.248671
-Negative log-likelihood at call 109: 4.362714
+Sum of squared residuals at call 109: 4.362714
85.00276 -0.7774913 -4.025819 1.248671
85.00272 -0.7774913 -4.025819 1.248671
85.00274 -0.7774904 -4.025819 1.248671
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 84500b54..9e912a28 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
MeasurementUnits: % AR
TimeUnits: days
Comments: Created using mkin::CAKE_export
-Date: 2019-04-10
+Date: 2019-04-24
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 1d669d43..b0a6bb6d 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -10,10 +10,10 @@ d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
Model predictions using solution type analytical
-Fitted with method using test 0 model solutions performed in test time 0 s
+Fitted using test 0 model solutions performed in test time 0 s
Error model:
-NULL
+Constant variance
Starting values for parameters to be optimised:
value type
@@ -61,7 +61,7 @@ k2 0.01785 7.636 7.901e-04 0.01241 0.02568
g 0.85390 83.310 6.221e-08 0.82310 0.88020
sigma 0.69620 4.243 6.618e-03 0.24060 1.15200
-Chi2 error levels in percent:
+FOCUS Chi2 error levels in percent:
err.min n.optim df
All data 2.661 4 5
parent 2.661 4 5
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 3a49078c..a282f5e7 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -74,22 +74,3 @@ test_that("Fits without internal transformations are correct for FOCUS D", {
# References:
# Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
# zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
-
-test_that("The t-value for fits using internal transformations corresponds with results from FME, synthetic data", {
- skip_on_cran()
- m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
- M1 = mkinsub("SFO"),
- M2 = mkinsub("SFO"),
- use_of_ff = "min", quiet = TRUE)
-
- fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff,
- synthetic_data_for_UBA_2014[[12]]$data,
- quiet = TRUE)
-
- skip("Hessian matrices and df calculations differ from those in FME")
- # Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test
- expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5),
- c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588,
- f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890,
- k1 = 16.1450, k2 = 8.1747))
-})
diff --git a/tests/testthat/test_logistic.R b/tests/testthat/test_logistic.R
index 9f50f32e..5a89fbf5 100644
--- a/tests/testthat/test_logistic.R
+++ b/tests/testthat/test_logistic.R
@@ -34,13 +34,3 @@ test_that("The logistic model fit is reproducible", {
dtx <- endpoints(m)$distimes["parent", ]
expect_equivalent(dtx, c(36.865, 62.415, 4297.854, 10.833), tolerance = 0.001)
})
-
-test_that("The logistic fit can be done via differential equation", {
- # This is slow as we did not implement conversion to C
- # because it is unlikely we will use the logistic model with metabolites
- skip("Skip slow fit of logistic model using deSolve without compilation")
- m_2 <- mkinfit("logistic", d_2_1[[1]], solution_type = "deSolve",
- quiet = TRUE)
- dtx_2 <- endpoints(m_2)$distimes["parent", ]
- expect_equivalent(dtx_2, c(36.865, 62.415, 4297.854, 10.833), tolerance = 0.001)
-})

Contact - Imprint