From 247046327c7d859e61d32c798cb6f82761d7b1ad Mon Sep 17 00:00:00 2001
From: Sebastian Henz <sebastian.henz@ufz.de>
Date: Mon, 16 Mar 2020 15:06:27 +0100
Subject: [PATCH] Set default "which" value to NA. Use empty vectors or NULL to
show just the axes.
---
DESCRIPTION | 4 ++--
NEWS.md | 5 +++++
R/plot_ecxsys.R | 5 +++--
R/plot_effect.R | 12 ++++++------
R/plot_stress.R | 12 ++++++------
man/plot_ecxsys.Rd | 9 +++++----
6 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b396809..ee2ef22 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: stressaddition
Type: Package
Title: Modeling Tri-Phasic Concentration-Response Relationships
-Version: 2.4.0
-Date: 2020-03-13
+Version: 2.4.1
+Date: 2020-03-16
Authors@R: c(person("Sebastian",
"Henz",
role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index f43297f..bf1b000 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# stressaddition 2.4.1
+
+* Fixed unintended behaviour in `plot_effect()` and `plot_stress()` where supplying an empty vector caused the four standard curves to show. Now setting `which` to an empty vector or `NULL` shows just the axes. The default value is NA.
+* Renamed the `mixture_effect` column in the `predict_mixture` output data frame to `effect`.
+
# stressaddition 2.4.0
* Improved `plot_effect()` and `plot_stress()`. You can now control whether the observed values (the points) should be plotted using the `which` argument.
diff --git a/R/plot_ecxsys.R b/R/plot_ecxsys.R
index f1cd7ca..e3d1f3e 100644
--- a/R/plot_ecxsys.R
+++ b/R/plot_ecxsys.R
@@ -31,8 +31,9 @@
#' \code{model$curves} data frame. There is also \code{"effect_tox_observed"}
#' and \code{"effect_tox_env_observed"} for the observed effects and
#' \code{"sys_tox_observed"} and \code{"sys_tox_env_observed"} for the
-#' observed Sys. The default \code{NULL} only plots the most important curves.
-#' Use \code{which = "all"} to display all curves.
+#' observed Sys. The default \code{NA} only plots the most important curves.
+#' Use \code{which = "all"} to display all curves. An empty vector or
+#' \code{NULL} creates just the axes.
#'
#' @param show_legend Should the plot include a legend? Defaults to \code{FALSE}
#' because it may cover some parts of the plot depending on the plot size and
diff --git a/R/plot_effect.R b/R/plot_effect.R
index 0645f03..942b3cc 100644
--- a/R/plot_effect.R
+++ b/R/plot_effect.R
@@ -20,7 +20,7 @@
#' @rdname plot_ecxsys
#' @export
plot_effect <- function(model,
- which = NULL,
+ which = NA,
show_legend = FALSE,
xlab = "concentration",
ylab = "effect",
@@ -32,7 +32,7 @@ plot_effect <- function(model,
curve_names[startsWith(curve_names, "effect")],
"effect_tox_observed", "effect_tox_env_observed" # the observed points
)
- if (is.null(which)) {
+ if (length(which) == 1 && is.na(which)) {
which <- c("effect_tox", "effect_tox_sys", "effect_tox_observed")
if (model$with_env) {
which <- c(which, "effect_tox_env", "effect_tox_env_sys",
@@ -43,12 +43,12 @@ plot_effect <- function(model,
stop("'all' must not be combined with other curve names.")
}
which <- valid_names
+ } else if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
+ warning("'which' contains names with 'env' but the model was built ",
+ "without environmental effects.")
+ which <- which[which %in% valid_names]
} else if (any(!which %in% valid_names)) {
warning("Argument 'which' contains invalid names.")
- if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
- warning("'which' contains names with 'env' but the model was",
- " built without environmental effects.")
- }
which <- which[which %in% valid_names]
}
diff --git a/R/plot_stress.R b/R/plot_stress.R
index 296f90a..152b0a3 100644
--- a/R/plot_stress.R
+++ b/R/plot_stress.R
@@ -20,7 +20,7 @@
#' @rdname plot_ecxsys
#' @export
plot_stress <- function(model,
- which = NULL,
+ which = NA,
show_legend = FALSE,
xlab = "concentration",
ylab = "stress",
@@ -32,7 +32,7 @@ plot_stress <- function(model,
curve_names[startsWith(curve_names, "stress") | startsWith(curve_names, "sys")],
"sys_tox_observed", "sys_tox_env_observed" # the observed points
)
- if (is.null(which)) {
+ if (length(which) == 1 && is.na(which)) {
which <- c("sys_tox", "sys_tox_observed")
if (model$with_env) {
which <- c(which, "sys_tox_env", "sys_tox_env_observed")
@@ -42,12 +42,12 @@ plot_stress <- function(model,
stop("'all' must not be combined with other curve names.")
}
which <- valid_names
+ } else if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
+ warning("'which' contains names with 'env' but the model was built ",
+ "without environmental effects.")
+ which <- which[which %in% valid_names]
} else if (any(!which %in% valid_names)) {
warning("Argument 'which' contains invalid names.")
- if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
- warning("'which' contains names with 'env' but the model was",
- " built without environmental effects.")
- }
which <- which[which %in% valid_names]
}
diff --git a/man/plot_ecxsys.Rd b/man/plot_ecxsys.Rd
index 1c9c32f..1b5e970 100644
--- a/man/plot_ecxsys.Rd
+++ b/man/plot_ecxsys.Rd
@@ -8,7 +8,7 @@
\usage{
plot_effect(
model,
- which = NULL,
+ which = NA,
show_legend = FALSE,
xlab = "concentration",
ylab = "effect",
@@ -17,7 +17,7 @@ plot_effect(
plot_stress(
model,
- which = NULL,
+ which = NA,
show_legend = FALSE,
xlab = "concentration",
ylab = "stress",
@@ -31,8 +31,9 @@ plot_stress(
\code{model$curves} data frame. There is also \code{"effect_tox_observed"}
and \code{"effect_tox_env_observed"} for the observed effects and
\code{"sys_tox_observed"} and \code{"sys_tox_env_observed"} for the
-observed Sys. The default \code{NULL} only plots the most important curves.
-Use \code{which = "all"} to display all curves.}
+observed Sys. The default \code{NA} only plots the most important curves.
+Use \code{which = "all"} to display all curves. An empty vector or
+\code{NULL} creates just the axes.}
\item{show_legend}{Should the plot include a legend? Defaults to \code{FALSE}
because it may cover some parts of the plot depending on the plot size and
--
GitLab