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# 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)
})
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