Some test fixes

4 files changed, 11 insertions, 44 deletions

diff --git a/test.log b/test.log
index f39791ae..6105128f 100644
--- a/test.log
+++ b/test.log
@@ -6,7 +6,7 @@ Testing mkin
 ✔ |   2       | Export dataset for reading into CAKE
 ✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
-✔ |   7       | Fitting the SFORB model [3.6 s]
+✔ |   7       | Fitting the SFORB model [3.5 s]
 ✔ |   5       | Analytical solutions for coupled models [3.2 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  14       | Confidence intervals and p-values [1.2 s]
@@ -14,33 +14,7 @@ Testing mkin
 ✔ |   3       | Time step normalisation
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
-⠏ |   8 2     | Nonlinear mixed effects models                                                             
-LL by is "-1333.17 (df=13)"
-                           
-LL by is "-1333.17 (df=13)"
-                           
-LL by is "-1336.30 (df=13)"
-
✖ |  11 2     | Nonlinear mixed effects models [6.4 s]
-────────────────────────────────────────────────────────────────────────────────
-ERROR (test_mixed.R:11:3): Parent only models can be fitted using nonlinear mixed effects models
-Error: object 'sfo_saem_1' not found
-Backtrace:
- 1. base::summary(sfo_saem_1) test_mixed.R:11:2
-
-FAILURE (test_mixed.R:91:3): Print methods work
-Results have changed from known value recorded in 'print_sfo_saemix_1.txt'.
-
-old[6:11] vs new[6:13]
-  "Data:"
-  "264 observations of 1 variable(s) grouped in 15 datasets"
-  ""
-  "Likelihood computed by importance sampling"
-+ "                         "
-+ "LL by is \"-653.97 (df=6)\""
-  "   AIC  BIC logLik"
-  "  1320 1324   -654"
-  ""
-────────────────────────────────────────────────────────────────────────────────
+✔ |  31       | Nonlinear mixed effects models [27.5 s]
 ✔ |   2       | Test dataset classes mkinds and mkindsg
 ✔ |   1       | mkinfit features [0.3 s]
 ✔ |  12       | Special cases of mkinfit calls [0.8 s]
@@ -48,21 +22,16 @@ old[6:11] vs new[6:13]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
 ✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.6 s]
 ✔ |   9       | Nonlinear mixed-effects models [7.8 s]
-✖ |  15 1     | Plotting [1.9 s]
-────────────────────────────────────────────────────────────────────────────────
-FAILURE (test_plot.R:39:3): Plotting mkinfit and mmkin objects is reproducible
-Figures don't match: mixed-model-fit-for-nlme-object.svg
-
-────────────────────────────────────────────────────────────────────────────────
+✔ |  16       | Plotting [1.9 s]
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
 ✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
 ✔ |   9       | Hypothesis tests [7.3 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 48.1 s
+Duration: 69.3 s
 
-[ FAIL 3 | WARN 0 | SKIP 0 | PASS 183 ]
+[ FAIL 0 | WARN 0 | SKIP 0 | PASS 204 ]
diff --git a/tests/testthat/print_sfo_saemix_1.txt b/tests/testthat/print_sfo_saem_1.txt
index 9dd4f175..d341e9e7 100644
--- a/tests/testthat/print_sfo_saemix_1.txt
+++ b/tests/testthat/print_sfo_saem_1.txt
@@ -6,8 +6,6 @@ Data:
 264 observations of 1 variable(s) grouped in 15 datasets
 
 Likelihood computed by importance sampling
-                         
-LL by is "-653.97 (df=6)"
    AIC  BIC logLik
   1320 1324   -654
 
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 6fc6c2f0..7798be8a 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -88,7 +88,7 @@ test_that("Print methods work", {
   expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt")
   expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
   expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
-  expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt")
+  expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
 })
 
 test_that("nlme results are reproducible", {
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index b0bf2c8f..22f4307f 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,14 +35,14 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
-  plot_biphasic_nlme <- function() plot(dfop_nlme_1)
-  vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
-
   plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem)
   vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s)
 
   skip_on_travis()
 
+  plot_biphasic_nlme <- function() plot(dfop_nlme_1)
+  vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
+
   #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic))
   # Biphasic fits with lots of data and fits have lots of potential for differences
   plot_biphasic_nlme <- function() plot(nlme_biphasic)