README.md

In BastiHz/stressaddition: Modelling Tri-Phasic Concentration-Response Relationships

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. Modeling the synergistic effects of toxicant mixtures. Environ Sci Eur 32, 119 (2020).

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 available from CRAN:

install.packages("stressaddition")

You can also get the development version (potentially unstable) from GitLab:

install.packages("remotes")
remotes::install_gitlab("oekotox/stressaddition", host = "git.ufz.de")

Alternatively, there are binary and source builds of the current release and older versions available for download from the releases page.

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 under the influence of toxicant and system stress and the LC10 under the influence of toxicant, environmental and system stress:

lc(model_a, "survival_tox_sys", 50)
#> $response
#> [1] 44.95368
#> 
#> $concentration
#> [1] 3.375735
lc(model_a, "survival_tox_env_sys", 10)
#> $response
#> [1] 26.41904
#> 
#> $concentration
#> [1] 0.0008571244

Plot the survival and the system stresses:

par(mfrow = c(2, 1), mar = c(4, 4, 0.5, 0.1))
plot_survival(model_a)
plot_stress(model_a)

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  0.00000

Citation

Please cite this package if you use it in your analysis. See citation("stressaddition") for details.

Copyright 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/.

BastiHz/stressaddition documentation built on Dec. 31, 2020, 9:53 a.m.