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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-04 10:06:34 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-04 10:06:34 +0100
commitf24a86c1f33e06c8114021c5c3956b5f7c400c18 (patch)
tree50b69b4052aa2e897ba866aa3b0c481400e26296 /tests/testthat
parent91ef22b6c98b96a9954dfe0a9914c45b41ce2af4 (diff)
Revert to use starting values for random effects in nlme.mmkin
Diffstat (limited to 'tests/testthat')
-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
5 files changed, 4 insertions, 14 deletions
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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