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-rw-r--r--test.log29
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_nlme.R7
3 files changed, 16 insertions, 22 deletions
diff --git a/test.log b/test.log
index 877d5193..09dd4c3f 100644
--- a/test.log
+++ b/test.log
@@ -7,42 +7,33 @@ Testing mkin
✔ | 4 | Fitting the SFORB model [1.7 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [9.4 s]
-✔ | 14 | Error model fitting [37.5 s]
+✔ | 14 | Error model fitting [38.4 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s]
✔ | 1 | Fitting the logistic model [0.9 s]
✔ | 1 | Test dataset class mkinds used in gmkin
-✔ | 12 | Special cases of mkinfit calls [2.3 s]
+✔ | 12 | Special cases of mkinfit calls [2.4 s]
✔ | 9 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.3 s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✖ | 0 1 | Nonlinear mixed-effects models [1.3 s]
-────────────────────────────────────────────────────────────────────────────────
-test_nlme.R:37: error: nlme_function works correctly
-konnte Funktion "nlme_f" nicht finden
-Backtrace:
- 1. nlme::nlme(...) tests/testthat/test_nlme.R:37:2
- 2. nlme::nlme.formula(...)
- 3. [ base::eval(...) ] with 1 more call
- 5. [ base::eval(...) ] with 1 more call
-────────────────────────────────────────────────────────────────────────────────
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.2 s]
+✔ | 3 | Nonlinear mixed-effects models [2.1 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
✔ | 3 | Summary
✔ | 11 | Plotting [0.6 s]
✔ | 4 | AIC calculation
✔ | 2 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s]
-✔ | 7 1 | Hypothesis tests [31.9 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
+✔ | 7 1 | Hypothesis tests [34.0 s]
────────────────────────────────────────────────────────────────────────────────
test_tests.R:60: skip: We can do a likelihood ratio test using an update specification
Reason: This errors out if called by testthat while it works in a normal R session
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 111.4 s
+Duration: 115.8 s
-OK: 138
-Failed: 1
+OK: 141
+Failed: 0
Warnings: 0
Skipped: 1
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index f492a57f..118f61f4 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: 2020-04-07
+Date: 2020-04-08
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index b3c41f00..31db92e1 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -26,7 +26,11 @@ test_that("nlme_function works correctly", {
mean_dp <- mean_degparms(f)
grouped_data <- nlme_data(f)
+
nlme_f <- nlme_function(f)
+ # The following assignment was introduced for nlme as evaluated by testthat
+ # to find the function
+ assign("nlme_f", nlme_f, pos = globalenv())
m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
data = grouped_data,
@@ -58,6 +62,5 @@ test_that("nlme_function works correctly", {
m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
- # update(m_nlme_mkin) # works
-
+ expect_silent(tmp <- update(m_nlme_mkin))
})

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