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-rw-r--r--R/nlme.mmkin.R2
-rw-r--r--test.log10
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt4
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_eigen.txt4
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R2
-rw-r--r--tests/testthat/test_nlme.R6
7 files changed, 10 insertions, 20 deletions
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index e8418ebd..6d24a044 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -150,7 +150,7 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
thisCall[["data"]] <- nlme_data(model)
if (missing(start)) {
- thisCall[["start"]] <- mean_degparms(model, random = FALSE)
+ thisCall[["start"]] <- mean_degparms(model, random = TRUE)
}
thisCall[["fixed"]] <- lapply(as.list(dp_names), function(el)
diff --git a/test.log b/test.log
index 10c5645e..b356bac5 100644
--- a/test.log
+++ b/test.log
@@ -5,11 +5,11 @@ Testing mkin
✔ | 2 | Export dataset for reading into CAKE
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.4 s]
+✔ | 7 | Fitting the SFORB model [3.3 s]
✔ | 5 | Analytical solutions for coupled models [3.2 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [1.0 s]
-✔ | 14 | Error model fitting [4.2 s]
+✔ | 14 | Error model fitting [4.1 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
@@ -17,7 +17,7 @@ Testing mkin
✔ | 12 | Special cases of mkinfit calls [0.6 s]
✔ | 8 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.4 s]
-✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.2 s]
+✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.1 s]
────────────────────────────────────────────────────────────────────────────────
test_nafta.R:25: skip: Test data from Appendix B are correctly evaluated
Reason: getRversion() < "4.1.0" is TRUE
@@ -25,7 +25,7 @@ Reason: getRversion() < "4.1.0" is TRUE
test_nafta.R:53: skip: Test data from Appendix D are correctly evaluated
Reason: getRversion() < "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
-✔ | 9 | Nonlinear mixed-effects models [7.8 s]
+✔ | 9 | Nonlinear mixed-effects models [7.7 s]
✔ | 0 1 | Plotting [0.7 s]
────────────────────────────────────────────────────────────────────────────────
test_plot.R:24: skip: Plotting mkinfit and mmkin objects is reproducible
@@ -40,7 +40,7 @@ Reason: getRversion() < "4.1.0" is TRUE
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 37.8 s
+Duration: 37.5 s
OK: 146
Failed: 0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index b8828b57..c7cb6d41 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: 2020-10-27
+Date: 2020-11-04
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index 0b31a81f..9245c40b 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
@@ -33,10 +33,6 @@ Fixed parameter values:
value type
m1_0 0 state
-
-Warning(s):
-Shapiro-Wilk test for standardized residuals: p = 0.0165
-
Results:
AIC BIC logLik
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
index 8ced5c4d..141f57a1 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
@@ -33,10 +33,6 @@ Fixed parameter values:
value type
m1_0 0 state
-
-Warning(s):
-Shapiro-Wilk test for standardized residuals: p = 0.0165
-
Results:
AIC BIC logLik
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 0a7e5219..faf473c4 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -4,7 +4,7 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
test_that("Fits without formation fractions are correct for FOCUS D", {
expect_warning(
- fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE),
+ fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, test_residuals = TRUE),
"Shapiro-Wilk")
expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2),
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index 5a8db142..4fd8e53f 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -59,12 +59,10 @@ test_that("nlme_function works correctly", {
expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients)
- anova_nlme <- anova(m_nlme_mmkin, m_nlme_raw) # mmkin needs to go first as we had
- # to adapt the method due to
- # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
+ anova_nlme <- anova(m_nlme_raw, m_nlme_mmkin)
# We get a slightly lower AIC with the improved starting values used within
- # nlme.mmkin
+ # nlme.mmkin, specifying also random effects
expect_lt(anova_nlme["m_nlme_mmkin", "AIC"],
anova_nlme["m_nlme_raw", "AIC"])

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