Improve tests, remove geometric_mean

1 files changed, 75 insertions, 0 deletions

diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
new file mode 100644
index 00000000..c1d46dcb
--- /dev/null
+++ b/tests/testthat/setup_script.R
@@ -0,0 +1,75 @@
+# Copyright (C) 2016-2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+require(mkin)
+require(testthat)
+
+# Per default (on my box where I set NOT_CRAN) use all cores minus one
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+  n_cores <- parallel::detectCores() - 1
+} else {
+  n_cores <- 1
+}
+
+# We are only allowed one core on travis, but they also set NOT_CRAN=true
+if (Sys.getenv("TRAVIS") != "") n_cores = 1
+
+# On Windows we would need to make a cluster first
+if (Sys.info()["sysname"] == "Windows") n_cores = 1
+
+# mmkin object of parent fits for tests
+models <- c("SFO", "FOMC", "DFOP", "HS")
+fits <- mmkin(models,
+  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+  quiet = TRUE, cores = n_cores)
+
+# One metabolite
+SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                   m1 = list(type = "SFO"), quiet = TRUE)
+SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                      m1 = list(type = "SFO"),
+                      use_of_ff = "max", quiet = TRUE)
+
+f_sfo_sfo <- mkinfit(SFO_SFO,
+  subset(FOCUS_2006_D, value != 0),
+  quiet = TRUE)
+
+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
+
+m_synth_SFO_lin <- mkinmod(
+  parent = mkinsub("SFO", "M1"),
+  M1 = mkinsub("SFO", "M2"),
+  M2 = mkinsub("SFO"),
+  use_of_ff = "max", quiet = TRUE)
+
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+  M1 = mkinsub("SFO"),
+  M2 = mkinsub("SFO"),
+  use_of_ff = "max", quiet = TRUE)
+
+f_SFO_lin_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
+f_SFO_lin_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
+  error_model = "const", error_model_algorithm = "direct")
+