Default to analytical for coupled models if available

This revealed that transforming rates is necessary for fitting
the analytical solution of the SFO-SFO model to the FOCUS D dataset.

Benchmarks show that fitting coupled models with deSolve got a bit
slower through the latest changes

2 files changed, 16 insertions, 7 deletions

diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index f113a668..d41f0a9f 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: 2020-05-09
+Date: 2020-05-10
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index f3b12bd9..be2806de 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -2,19 +2,22 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
 
 # Results are from p. 40
 
+# Avoid warnings due to the zero value in the data for m1 at time zero
+FOCUS_D <- subset(FOCUS_2006_D, value != 0)
+
 test_that("Fits without formation fractions are correct for FOCUS D", {
-  fit.default <- expect_warning(mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE), "value of zero")
+  fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE)
 
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2),
+  expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2),
                c(7.02, 23.33))
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1),
+  expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["m1", ]), 1),
                c(131.8, 437.7))
 
 })
 
 test_that("Fits with formation fractions are correct for FOCUS D", {
   skip_on_cran()
-  fit.ff <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE), "value of zero")
+  fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE)
   expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)),
                     c(99.60, 0.0987, 0.0053, 0.5145))
 
@@ -30,8 +33,15 @@ test_that("Fits with formation fractions are correct for FOCUS D", {
 test_that("Fits without internal transformations are correct for FOCUS D", {
   skip_on_cran()
   expect_warning(
+    # Analytical solutions (now the default for SFO_SFO with formation fractions)
+    # return NA at some point not internally transforming rates
+    expect_error(fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_D,
+      transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE)))
+
+  expect_warning(
     fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_2006_D,
-      transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE),
+      transform_fractions = FALSE, transform_rates = FALSE,
+      quiet = TRUE, solution_type = "deSolve"),
     "sum of formation fractions")
 
   expect_equivalent(round(fit.ff.notrans$bparms.optim, c(2, 4, 4, 4)),
@@ -40,7 +50,6 @@ test_that("Fits without internal transformations are correct for FOCUS D", {
   expect_equivalent(round(100 * mkinerrmin(fit.ff.notrans)$err.min, 2),
                     c(6.40, 6.46, 4.69))
 
-
   expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["parent", ]), 2),
                c(7.02, 23.33))
   expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["m1", ]), 1),