From 23461dddcc6a1858f1c9c9052512f22485d08842 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 9 Apr 2020 09:38:01 +0200
Subject: Try mkinerrplot for obs and tc on Travis again

---
 tests/testthat/test_nlme.R              | 59 +++++++++++++++++++++++++++++++++
 tests/testthat/test_plots_summary_twa.R |  1 -
 2 files changed, 59 insertions(+), 1 deletion(-)

(limited to 'tests')

diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index 31db92e1..0d1fcd6d 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -64,3 +64,62 @@ test_that("nlme_function works correctly", {
 
   expect_silent(tmp <- update(m_nlme_mkin))
 })
+
+test_that("nlme_function works correctly in other cases", {
+
+  dt50_in <- c(400, 800, 1200, 1600, 2000)
+  dt50_in_geomean <- geomean(dt50_in)
+  k_in <- log(2) / dt50_in
+  SFO <- mkinmod(parent = mkinsub("SFO"))
+  pred_sfo <- function(k) {
+    mkinpredict(SFO,
+      c(k_parent_sink = k),
+      c(parent = 100),
+      sampling_times)
+  }
+  ds_me_sfo <- mapply(pred_sfo, k_in, SIMPLIFY = FALSE)
+  add_err_5 <- function(i) {
+    add_err(ds_me_sfo[[i]], sdfunc = function(value) 5, n = 3, seed = i + 1)
+  }
+  ds_me_sfo_5 <- sapply(1:5, add_err_5)
+  names(ds_me_sfo_5) <- paste("Dataset", 1:15)
+  dimnames(ds_me_sfo_5) <- list(Subset = 1:3, DT50 = dt50_in)
+
+  f_me_sfo_5 <- mmkin("SFO", ds_me_sfo_5)
+
+  ds_me_sfo_5_grouped_mkin <- nlme_data(f_me_sfo_5)
+  ds_me_sfo_5_mean_dp <- mean_degparms(f_me_sfo_5)
+  me_sfo_function <- nlme_function(f_me_sfo_5)
+
+  f_nlme_sfo_5_all_mkin <- nlme(value ~ me_sfo_function(name, time,
+      parent_0, log_k_parent_sink),
+    data = ds_me_sfo_5_grouped,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = ds_me_sfo_5_mean_dp)
+
+  f_nlme_sfo_5 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+    data = ds_me_sfo_5_grouped_mkin,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = ds_me_sfo_5_mean_dp)
+
+  expect_equal(f_nlme_sfo_5_all_mkin$coefficients, f_nlme_sfo_5$coefficients)
+
+  # With less ideal starting values we get fits with lower AIC (not shown)
+  f_nlme_sfo_5_all_mkin_nostart <- nlme(value ~ me_sfo_function(name, time,
+      parent_0, log_k_parent_sink),
+    data = ds_me_sfo_5_grouped,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = c(parent_0 = 100, log_k_parent_sink = log(0.1)))
+
+  f_nlme_sfo_5_nostart <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+    data = ds_me_sfo_5_grouped_mkin,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = c(parent_0 = 100, log_k_parent_sink = log(0.1)))
+
+  expect_equal(f_nlme_sfo_5_all_mkin_nostart$coefficients, f_nlme_sfo_5_nostart$coefficients)
+
+})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 5917dd6e..77144665 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -111,7 +111,6 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
   vdiffr::expect_doppelganger("mkinerrplot for FOCUS C SFO", mkinerrplot_FOCUS_C_SFO)
   vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
   vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
-  skip_on_travis() # No idea why the following are different on Travis
   vdiffr::expect_doppelganger("plot_res for FOCUS D", plot_res_sfo_sfo)
   vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo)
   vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_tc", plot_errmod_fit_tc_1)
-- 
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