diff --git a/.Rbuildignore b/.Rbuildignore
index 99b26c0730c4eba1d039282415cd41244d6abbfe..a8d197a8a0fa8cbf9a7cddd418902d1671040e41 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -8,3 +8,4 @@
^\.gitlab$
^\.gitlab-ci\.yml$
^data-raw$
+^images$
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000000000000000000000000000000000000..24a8e87939aa53cdd833f6be7610cb4972e063ad
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+*.png filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
index eddaf3d24df4c6520b1ef99aa062c58441c54acb..065f56108d9a9934746a7a4d890cdb3ff7ab55ef 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,4 +4,3 @@
.Ruserdata
Notizen.md
-*.png
diff --git a/DESCRIPTION b/DESCRIPTION
index 0afe62bc06305f34888ce2b00ea438f4b536016b..2b2edea580c30293b9f01b79dbd488e439dbe50b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: stressaddition
Type: Package
Title: Modelling Tri-Phasic Concentration-Response Relationships
Version: 3.0.0
-Date: 2020-05-18
+Date: 2020-07-06
Authors@R: c(person("Sebastian",
"Henz",
role = c("aut", "cre"),
@@ -17,7 +17,7 @@ Authors@R: c(person("Sebastian",
role = "ctb",
comment = c(ORCID = "0000-0001-6581-1654")),
person("Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ",
- role = c("cph")))
+ role = c("cph", "fnd")))
Description: The stress addition approach is an alternative to the traditional
concentration addition or effect addition models. It allows the modelling
of tri-phasic concentration-response relationships either as single toxicant
@@ -35,4 +35,4 @@ Imports:
plotrix
Suggests:
testthat (>= 2.1.0)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
diff --git a/README.md b/README.md
index b92fa6f9c2171c83e1872a05939b02a1ffb1b4f1..5e7da03c5546633c81db01e7347fafc13f388550 100644
--- a/README.md
+++ b/README.md
@@ -1,47 +1,84 @@
# stressaddition
-This is the R implementation of 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)](https://doi.org/10.1038/s41598-019-51645-4). It allows modeling of ecotoxicological experiments where the response shows signs of a hormesis effect.
+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()`.
-The EC<sub>x-SyS</sub> and Multi-TOX models from this package are also available as part of the [Indicate app](http://www.systemecology.eu/indicate) which offers a graphical user interface.
+`ecxsys()` implements **EC<sub>x-SyS</sub>**, 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)](https://doi.org/10.1038/s41598-019-51645-4). 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 EC<sub>x-SyS</sub> and Multi-TOX models are also available as part of the [Indicate app](http://www.systemecology.eu/indicate) which offers an easy to use graphical user interface.
## Installation
-Stressaddition is not yet on CRAN. You can install the most recent development version from GitLab using the remotes package:
+This package is not yet available on CRAN. Until then you can install the most recent version from GitLab using the remotes package:
``` r
install.packages("remotes")
remotes::install_gitlab("oekotox/stressaddition", host = "git.ufz.de")
```
-Alternatively there are binary and source builds of various versions downloadable from the [releases page](https://git.ufz.de/oekotox/stressaddition/-/releases).
-
-## Updating
-RStudio's integrated package updater won't detect updates in packages installed from GitHub or GitLab. I recommend running
-```r
-remotes::update_packages()
-```
-in regular intervals to check for updates from those sources.
+Alternatively, there are binary and source builds of various versions available for download from the [releases page](https://git.ufz.de/oekotox/stressaddition/-/releases).
## Citation
Please cite this package if you use it in your analysis. See `citation("stressaddition")` for details.
-## Example
-```r
+## Examples
+
+### EC<sub>x-SyS</sub>
+Model a concentration-response relationship with hormesis:
+```R
library(stressaddition)
-model <- ecxsys(
+model_a <- ecxsys(
concentration = c(0, 0.05, 0.5, 5, 30),
- hormesis_concentration = 0.5,
survival_tox_observed = c(90, 81, 92, 28, 0),
- survival_tox_env_observed = c(29, 27, 33, 5, 0)
+ survival_tox_env_observed = c(29, 27, 33, 5, 0),
+ hormesis_concentration = 0.5
)
+```
-# Plot the effect and the system stress:
-par(mfrow = c(2, 1))
-plot_survival(model)
-plot_stress(model)
+Calculate the LC<sub>50</sub> and LC<sub>10</sub>:
+```R
+# 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] 0.0008571244
+```
-# The LC50 under the influence of toxicant and system tress:
-lc(model, "survival_tox_sys", 50)
+Plot the survival and the system stresses:
+```R
+par(mfrow = c(2, 1))
+plot_survival(model_a, show_legend = TRUE)
+plot_stress(model_a, show_legend = TRUE)
+```
+
-# The LC10 under the influence of toxicant, system and environmental tress:
-lc(model, "survival_tox_env_sys", 10)
+### Multi-TOX
+Define an additional single toxicant model and calculate the survival for some binary concentration mixtures:
+```R
+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
```
## Copyright and License
diff --git a/images/example.png b/images/example.png
new file mode 100644
index 0000000000000000000000000000000000000000..224712bdba8ff8ad2ef41e5d8ab18dd4d96be55c
--- /dev/null
+++ b/images/example.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:16a0b141b74374575d019a95d37ff881dca10ab45aaf3291c9a0c6e7f2124a00
+size 12905
diff --git a/man/stressaddition-package.Rd b/man/stressaddition-package.Rd
index 795b1eea48463eb5d0f68d2d6295a164542695bd..cf59dfb6ce4127e8a3c63fc9b2ce9acd5a35c1b7 100644
--- a/man/stressaddition-package.Rd
+++ b/man/stressaddition-package.Rd
@@ -47,7 +47,7 @@ Authors:
Other contributors:
\itemize{
\item Naeem Shahid (\href{https://orcid.org/0000-0001-6581-1654}{ORCID}) [contributor]
- \item Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ [copyright holder]
+ \item Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ [copyright holder, funder]
}
}