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# Copyright (C) 2016 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("Fitting the FOMC model with large parameter correlation")
# Dataset that I ran across during my work and for which the calculation of the
# Jacobian failed. Data were slightly fuzzed.
FOMC_test <- data.frame(
name = "test_compound",
time = c(0, 14, 31, 59, 91),
value = c(45.8, 28.0, 28.5, 35.1, 35.6))
test_that("Fitting with large parameter correlation gives warnings", {
skip("Skip test for warnings triggered by large parameter correlation as it failed on r-forge")
# When fitting from the maximum, the Port algorithm does not converge (with
# default settings)
expect_warning(
fit.FOMC.Port <- mkinfit("FOMC", FOMC_test, method.modFit = "Port"),
"Optimisation by method Port did not converge")
# When we use Levenberg-Marquardt, we get a problem estimating the Jacobian
# for the untransformed model
expect_warning(
fit.FOMC.Marq <- mkinfit("FOMC", FOMC_test, method.modFit = "Marq"),
"Calculation of the Jacobian failed for the cost function of the untransformed model")
})
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