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author | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-21 14:34:45 +0100 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-21 14:50:27 +0100 |
commit | d89e3d22eb9dc383897b09e9c5aa1b57f65cdbf0 (patch) | |
tree | e81237fcbd996390eadd439295f2fb4b3874b0ab /tests | |
parent | f134599b4d2cd3558b887b7f06faf1dfb599196e (diff) |
Add the logistic model
Diffstat (limited to 'tests')
-rw-r--r-- | tests/testthat/test_logistic.R | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/tests/testthat/test_logistic.R b/tests/testthat/test_logistic.R new file mode 100644 index 00000000..1ea1013b --- /dev/null +++ b/tests/testthat/test_logistic.R @@ -0,0 +1,47 @@ +# 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("Fitting the logistic model") + +logistic <- mkinmod(parent = mkinsub("logistic")) + +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2) +parms_logistic_optim <- c(parent_0 = 100, parms_logistic) +d_logistic <- mkinpredict(logistic, + parms_logistic, c(parent = 100), + sampling_times) +d_2_1 <- add_err(d_logistic, + sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07), + n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456) + +test_that("The logistic model fit is reproducible", { + m <- mkinfit("logistic", d_2_1[[1]], quiet = TRUE) + dtx <- endpoints(m)$distimes["parent", ] + expect_equivalent(dtx, c(36.86533, 62.41511), tolerance = 0.00001) +}) + +test_that("The logistic fit can be done via differential equation", { + # This is slow as we did not implement conversion to C + # because it is unlikely we will use the logistic model with metabolites + skip("Skip slow fit of logistic model using deSolve without compilation") + m_2 <- mkinfit("logistic", d_2_1[[1]], solution_type = "deSolve", + quiet = TRUE) + dtx_2 <- endpoints(m_2)$distimes["parent", ] + expect_equivalent(dtx_2, c(36.86533, 62.41511), tolerance = 0.00001) +}) |