Refactor mkinfit, infrastructure work

mkinfit objects now include an ll() function to calculate the
log-likelihood. Part of the code was refactored, hopefully making it
easier to read and maintain. IRLS is currently the default algorithm for
the error model "obs", for no particular reason. This may be subject
to change when I get around to investigate.

Slow tests are now in a separate subdirectory and will probably
only be run by my own Makefile target.

Formatting of test logs is improved.

Roundtripping error model parameters works with a precision of 10% when
we use lots of replicates in the synthetic data (see slow tests). This
is not new in this commit, but as I think it is reasonable this
closes #7.

1 files changed, 51 insertions, 0 deletions

diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R
new file mode 100644
index 00000000..e5cc1954
--- /dev/null
+++ b/tests/testthat/test_confidence.R
@@ -0,0 +1,51 @@
+# Copyright (C) 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/>
+
+context("Confidence intervals and p-values")
+
+m_synth_SFO_lin <- mkinmod(
+  parent = mkinsub("SFO", "M1"),
+  M1 = mkinsub("SFO", "M2"),
+  M2 = mkinsub("SFO"),
+  use_of_ff = "max", quiet = TRUE)
+
+SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
+
+test_that("Confidence intervals are stable", {
+  f_1_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
+  f_1_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
+    error_model = "const", error_model_algorithm = "direct")
+
+  bpar_1 <- summary(f_1_mkin_ML)$bpar[, c("Estimate", "Lower", "Upper")]
+  # The reference used here is mkin 0.9.48.1
+  bpar_1_mkin_0.9 <-   read.table(text =
+"parent_0       102.0000 98.6000 106.0000
+k_parent         0.7390  0.6770   0.8070
+k_M1             0.2990  0.2560   0.3490
+k_M2             0.0202  0.0176   0.0233
+f_parent_to_M1   0.7690  0.6640   0.8480
+f_M1_to_M2       0.7230  0.6030   0.8180",
+col.names = c("parameter", "estimate", "lower", "upper"))
+
+  expect_equivalent(signif(bpar_1[1:6, "Estimate"], 3), bpar_1_mkin_0.9$estimate)
+
+  # Relative difference of lower bound of the confidence interval is < 0.02
+  expect_equivalent(bpar_1[1:6, "Lower"], bpar_1_mkin_0.9$lower,
+      scale = bpar_1_mkin_0.9$lower, tolerance = 0.02)
+  })
+