stressaddition
This R package makes it possible to model tri-phasic concentration-response relationships using the stress addition approach. It is useful for the analysis of ecotoxicological data where the traditional concentration addition or effect addition models are inadequate. Its main functions are ecxsys() and multi_tox().
ecxsys() implements ECx-SyS, the tri-phasic concentration-response model introduced in
Liess, M., Henz, S. & Knillmann, S. Predicting low-concentration effects of pesticides. Sci Rep 9, 15248 (2019). It is applicable to modelling ecotoxicological experiments with and without environmental stress where the response contains a hormesis effect.
multi_tox() implements Multi-TOX, a model for binary mixtures of toxicants where each toxicant exhibits a tri-phasic concentration-response relationship. See Liess, M., Henz, S., Shahid, N. (2020), Modelling the synergistic effects of toxicant mixtures. Manuscript submitted for publication.
The ECx-SyS and Multi-TOX models are also available as part of the Indicate app which offers an easy to use graphical user interface.
Installation
This package is not available on CRAN. You can install the most recent version from GitLab:
install.packages("remotes")
remotes::install_gitlab("oekotox/stressaddition", host = "git.ufz.de")Alternatively, there are binary and source builds of various versions available for download from the releases page.
Citation
Please cite this package if you use it in your analysis. See citation("stressaddition") for details.
Examples
ECx-SyS
Model a concentration-response relationship with hormesis:
library(stressaddition)
model_a <- ecxsys(
concentration = c(0, 0.05, 0.5, 5, 30),
survival_tox_observed = c(90, 81, 92, 28, 0),
survival_tox_env_observed = c(29, 27, 33, 5, 0),
hormesis_concentration = 0.5
)Calculate the LC50 and LC10:
# LC50 under the influence of toxicant and system stress:
lc(model_a, "survival_tox_sys", 50)
# $response
# [1] 44.95368
#
# $concentration
# [1] 3.375735
# LC10 under the influence of toxicant, environmental and system stress:
lc(model_a, "survival_tox_env_sys", 10)
# $response
# [1] 26.41904
#
# $concentration
# [1] 0.0008571244Plot the survival and the system stresses:
par(mfrow = c(2, 1))
plot_survival(model_a, show_legend = TRUE)
plot_stress(model_a, show_legend = TRUE)
Multi-TOX
Define an additional single toxicant model and calculate the survival for some binary concentration mixtures:
model_b <- ecxsys(
concentration = c(0, 0.01, 0.1, 1, 10, 100),
survival_tox_observed = c(96, 89, 91, 57, 9, 0),
hormesis_concentration = 0.1
)
multi_tox(
model_a,
model_b,
concentration_a = c(0.1, 0.3, 2, 15),
concentration_b = c(0.04, 0.1, 1, 13)
)[, 1:3]
# concentration_a concentration_b survival
# 1 0.1 0.04 84.44956
# 2 0.3 0.10 73.53734
# 3 2.0 1.00 13.38661
# 4 15.0 13.00 0.00000Copyright and License
Copyright (c) 2020,
Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ.
All rights reserved.
The code is a property of:
Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ
Registered Office: Leipzig
Registration Office: Amtsgericht Leipzig
Trade Register: Nr. B 4703
Chairman of the Supervisory Board: MinDirig'in Oda Keppler
Scientific Director: Prof. Dr. Georg Teutsch
Administrative Director: Dr. Sabine König
stressaddition 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 https://www.gnu.org/licenses/.