Revert to use starting values for random effects in nlme.mmkin

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"])