From c5878e0c561a93f36f8fdc64d5839db2a0527572 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 7 Apr 2020 20:25:03 +0200
Subject: Add some tests for the nlme convenience functions

---
 tests/testthat/FOCUS_2006_D.csf |  2 +-
 tests/testthat/test_nlme.R      | 63 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test_nlme.R

(limited to 'tests')

diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index fe5e481a..f492a57f 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: 2020-04-01
+Date: 2020-04-07
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
new file mode 100644
index 00000000..b3c41f00
--- /dev/null
+++ b/tests/testthat/test_nlme.R
@@ -0,0 +1,63 @@
+context("Nonlinear mixed-effects models")
+
+test_that("nlme_function works correctly", {
+
+  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+  m_SFO <- mkinmod(parent = mkinsub("SFO"))
+  d_SFO_1 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.1),
+    c(parent = 98), sampling_times)
+  d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
+  d_SFO_2 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.05),
+    c(parent = 102), sampling_times)
+  d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
+  d_SFO_3 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.02),
+    c(parent = 103), sampling_times)
+  d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
+
+  d1 <- add_err(d_SFO_1, function(value) 3, n = 1, seed = 123456)
+  d2 <- add_err(d_SFO_2, function(value) 2, n = 1, seed = 234567)
+  d3 <- add_err(d_SFO_3, function(value) 4, n = 1, seed = 345678)
+  ds <- c(d1 = d1, d2 = d2, d3 = d3)
+
+  f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)
+
+  mean_dp <- mean_degparms(f)
+  grouped_data <- nlme_data(f)
+  nlme_f <- nlme_function(f)
+
+  m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+    data = grouped_data,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = mean_dp)
+
+  m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
+    data = grouped_data,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = mean_dp)
+
+  expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients)
+
+  m_nlme_raw_up_1 <- update(m_nlme_raw, random = log_k_parent_sink ~ 1)
+  # The following two calls give an error although they should
+  # do the same as the call above
+  # The error occurs in the evaluation of the modelExpression in the
+  # call to .C(fit_nlme, ...)
+  # m_nlme_mkin_up_1 <- update(m_nlme_mkin, random = log_k_parent_sink ~ 1)
+  # m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
+  #   data = grouped_data,
+  #   fixed = parent_0 + log_k_parent_sink ~ 1,
+  #   random = log_k_parent_sink ~ 1,
+  #   start = mean_dp)
+
+  m_nlme_raw_up_2 <- update(m_nlme_raw, random = parent_0 ~ 1)
+  m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
+  expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
+
+  # update(m_nlme_mkin) # works
+
+})
-- 
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