From edb67f950d19862d0e97e8d183081e884933caf5 Mon Sep 17 00:00:00 2001
From: Sebastian Henz <sebastian.henz@ufz.de>
Date: Tue, 5 May 2020 14:15:53 +0200
Subject: [PATCH] Update the documentation, closes #27.

---
 R/ecxsys.R       | 7 +++++--
 R/multi_tox.R    | 7 ++++---
 README.md        | 5 +++--
 man/ecxsys.Rd    | 7 +++++--
 man/multi_tox.Rd | 7 ++++---
 5 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/R/ecxsys.R b/R/ecxsys.R
index 6d321cd..e1140ec 100644
--- a/R/ecxsys.R
+++ b/R/ecxsys.R
@@ -28,8 +28,11 @@
 
 #' ECx-SyS
 #'
-#' The ECx-SyS model for modeling concentration-survival relationships with
-#' hormesis.
+#' ECx-SyS is a model for tri-phasic concentration-response relationships where
+#' hormetic and subhormetic effects are observed at low concentrations. It
+#' expands the Stress Addition Model (SAM) by introducing system stress (SyS)
+#' which is negatively correlated with toxicant stress. See the publication for
+#' details.
 #'
 #' It is advised to complete the curve down to zero for optimal prediction.
 #' Therefore \code{survival_tox_observed} in the highest concentration should be
diff --git a/R/multi_tox.R b/R/multi_tox.R
index 01c4f8b..2681881 100644
--- a/R/multi_tox.R
+++ b/R/multi_tox.R
@@ -17,10 +17,11 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 
-#' Predict the survival of a mixture of two toxicants
+#' Predict the survival of binary toxicant mixtures
 #'
-#' Given the ECx-SyS models of two toxicants this method predicts the survival
-#' of different mixtures.
+#' The Multi-TOX model predicts the effects of binary toxicant mixtures taking
+#' into account three-phasic concentration-response relationships. See the
+#' publication for details.
 #'
 #' The predictions are symmetric, i.e. it does not matter which of the toxicant
 #' models is 1 or 2 as long as the concentration arguments are supplied in the
diff --git a/README.md b/README.md
index e2de897..ecd2ba5 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,8 @@
 # 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.
+[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.
+
+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.
 
 ## Installation
 Stressaddition is not on CRAN. You can install the most recent stable version from GitLab using the remotes package:
diff --git a/man/ecxsys.Rd b/man/ecxsys.Rd
index c31e438..0ff51dd 100644
--- a/man/ecxsys.Rd
+++ b/man/ecxsys.Rd
@@ -69,8 +69,11 @@ A list (of class ecxsys) containing many different objects of which
   }
 }
 \description{
-The ECx-SyS model for modeling concentration-survival relationships with
-hormesis.
+ECx-SyS is a model for tri-phasic concentration-response relationships where
+hormetic and subhormetic effects are observed at low concentrations. It
+expands the Stress Addition Model (SAM) by introducing system stress (SyS)
+which is negatively correlated with toxicant stress. See the publication for
+details.
 }
 \details{
 It is advised to complete the curve down to zero for optimal prediction.
diff --git a/man/multi_tox.Rd b/man/multi_tox.Rd
index 62ecbdd..cc443d1 100644
--- a/man/multi_tox.Rd
+++ b/man/multi_tox.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/multi_tox.R
 \name{multi_tox}
 \alias{multi_tox}
-\title{Predict the survival of a mixture of two toxicants}
+\title{Predict the survival of binary toxicant mixtures}
 \usage{
 multi_tox(
   model_a,
@@ -34,8 +34,9 @@ A data frame with columns of the supplied concentrations and the
   corresponding mixture survival and stresses.
 }
 \description{
-Given the ECx-SyS models of two toxicants this method predicts the survival
-of different mixtures.
+The Multi-TOX model predicts the effects of binary toxicant mixtures taking
+into account three-phasic concentration-response relationships. See the
+publication for details.
 }
 \details{
 The predictions are symmetric, i.e. it does not matter which of the toxicant
-- 
GitLab