Add a lack-of-fit test

- Switch an example dataset in the test setup to a dataset with
replicates, adapt tests
- Skip the test for lrtest with an update specification as it does not
only fail when pkgdown generates static help pages, but also in testthat

4 files changed, 30 insertions, 11 deletions

diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 528e2b61..09940aa3 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: 2019-11-05
+Date: 2019-11-09
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 9becdd2a..e33f4af7 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -32,9 +32,6 @@ f_1_mkin_trans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)
 f_1_mkin_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE,
   transform_rates = FALSE)
 
-f_2_mkin <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
-f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = FOCUS_2006_C)
-
 # mmkin object of parent fits for tests
 models <- c("SFO", "FOMC", "DFOP", "HS")
 fits <- mmkin(models,
@@ -62,11 +59,14 @@ f_sfo_sfo.ff <- mkinfit(SFO_SFO.ff,
   subset(FOCUS_2006_D, value != 0),
   quiet = TRUE)
 
-# Two metabolites
 SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
 DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
 
+f_2_mkin <- mkinfit("DFOP", DFOP_par_c, quiet = TRUE)
+f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = subset(DFOP_par_c, name == "parent"))
+f_2_anova <- lm(value ~ as.factor(time), data = subset(DFOP_par_c, name == "parent"))
+
+# Two metabolites
 m_synth_SFO_lin <- mkinmod(
   parent = mkinsub("SFO", "M1"),
   M1 = mkinsub("SFO", "M2"),
diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R
index a2bf1401..e85fdb7a 100644
--- a/tests/testthat/test_confidence.R
+++ b/tests/testthat/test_confidence.R
@@ -54,11 +54,12 @@ test_that("Quadratic confidence intervals for rate constants are comparable to v
   # Another case:
   se_mkin_2 <- summary(f_2_mkin)$par[1:4, "Std. Error"]
   se_nls_2 <- summary(f_2_nls)$coefficients[, "Std. Error"]
-  # Here we the ratio of standard errors can be explained by the same
+  # Here the ratio of standard errors can be explained by the same
   # principle up to about 3%
+  nobs_DFOP_par_c_parent <- nrow(subset(DFOP_par_c, name == "parent"))
   expect_equivalent(
     se_nls_2[c("lrc1", "lrc2")] / se_mkin_2[c("log_k1", "log_k2")],
-    rep(sqrt(nrow(FOCUS_2006_C) / (nrow(FOCUS_2006_C) - 4)), 2),
+    rep(sqrt(nobs_DFOP_par_c_parent / (nobs_DFOP_par_c_parent - 4)), 2),
     tolerance = 0.03)
 })
 
@@ -73,7 +74,7 @@ test_that("Likelihood profile based confidence intervals work", {
    }
    f_mle <- stats4::mle(f_nll, start = as.list(parms(f)), nobs = nrow(FOCUS_2006_C))
 
-   ci_mkin_1_p_0.95 <- confint(f, method = "profile", level = 0.95, 
+   ci_mkin_1_p_0.95 <- confint(f, method = "profile", level = 0.95,
      cores = n_cores, quiet = TRUE)
 
    # Magically, we get very similar boundaries as stats4::mle
diff --git a/tests/testthat/test_tests.R b/tests/testthat/test_tests.R
index 5a522f8e..bdc72f08 100644
--- a/tests/testthat/test_tests.R
+++ b/tests/testthat/test_tests.R
@@ -1,5 +1,20 @@
 context("Hypothesis tests")
 
+test_that("The lack-of-fit test works and can be reproduced using nls", {
+
+  expect_error(loftest(f_1_mkin_trans), "Not defined for fits to data without replicates")
+
+  loftest_mkin <- loftest(f_2_mkin)
+
+  # This code is inspired by Ritz and Streibig (2008) Nonlinear Regression using R, p. 64
+  Q <- as.numeric(- 2 * (logLik(f_2_nls) -  logLik(f_2_anova)))
+  df.Q <- df.residual(f_2_nls) - df.residual(f_2_anova)
+  p_nls <- 1 - pchisq(Q, df.Q)
+
+  expect_equal(loftest_mkin[["2", "Pr(>Chisq)"]], p_nls, tolerance = 1e-5)
+
+})
+
 test_that("The likelihood ratio test works", {
 
   expect_error(lrtest(f_1_mkin_trans, f_2_mkin), "not been fitted to the same data")
@@ -25,7 +40,7 @@ test_that("Updating fitted models works", {
     parent = mkinsub("DFOP", to = "A1"),
     A1 = mkinsub("SFO", to = "A2"),
     A2 = mkinsub("SFO"),
-    use_of_ff = "max"
+    use_of_ff = "max", quiet = TRUE
   )
 
   f_soil_1_tc <- mkinfit(dfop_sfo_sfo,
@@ -41,6 +56,9 @@ test_that("Updating fitted models works", {
 })
 
 test_that("We can do a likelihood ratio test using an update specification", {
+  skip("This errors out if called by testthat while it works in a normal R session")
   test_2_mkin_k2 <- lrtest(f_2_mkin, fixed_parms = c(k2 = 0))
-  expect_equivalent(test_2_mkin_k2[["2", "Pr(>Chisq)"]], 1.139e-6, tolerance = 1e-8)
+  expect_equivalent(test_2_mkin_k2[["2", "Pr(>Chisq)"]], 4.851e-8, tolerance = 1e-8)
+  test_2_mkin_tc <- lrtest(f_2_mkin, error_model = "tc")
+  expect_equivalent(test_2_mkin_tc[["2", "Pr(>Chisq)"]], 7.302e-5, tolerance = 1e-7)
 })