From 26e97b199fa32f01e3a2bffafd7fa4b193f23c52 Mon Sep 17 00:00:00 2001
From: Sebastian Henz <sebastian.henz@ufz.de>
Date: Mon, 19 Oct 2020 16:48:28 +0200
Subject: [PATCH] Refactor the "which" argument in the plot functions closes
#57 Use the names as default values. NA will draw only the axes. Update
documentation.
---
DESCRIPTION | 4 ++--
NEWS.md | 7 +++++++
R/plot_ecxsys.R | 17 +++++++++--------
R/plot_stress.R | 31 +++++++++++++------------------
R/plot_survival.R | 34 +++++++++++++++-------------------
man/plot_ecxsys.Rd | 22 ++++++++++++----------
6 files changed, 58 insertions(+), 57 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index e6f968e..fdf2225 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: stressaddition
Type: Package
Title: Modelling Tri-Phasic Concentration-Response Relationships
-Version: 3.0.3
-Date: 2020-09-21
+Version: 3.1.0
+Date: 2020-10-19
Authors@R: c(person("Sebastian",
"Henz",
role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index beb7e46..983f36a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,14 @@
+# stressaddition 3.1.0
+
+* Improved the documentation of the `which` argument in `plot_survival()` and `plot_stress()`.
+* Changed the default value of the `which` argument in the plot functions. Now it contains the proper default curve names. If it is `NA` only the axes and labels will get drawn.
+
+
# stressaddition 3.0.3
* Added references to the journal article about the Multi-Tox model which was recently published.
+
# stressaddition 3.0.2
* Fixed a bug where the plotting functions printed `NULL` to the console.
diff --git a/R/plot_ecxsys.R b/R/plot_ecxsys.R
index 15658e9..a35f985 100644
--- a/R/plot_ecxsys.R
+++ b/R/plot_ecxsys.R
@@ -26,14 +26,15 @@
#'
#' @name plot_ecxsys
#'
-#' @param model The object returned from \code{\link{ecxsys}}.
-#' @param which A vector of names to plot. Allowed are the column names of the
-#' \code{model$curves} data frame. There is also
-#' \code{"survival_tox_observed"} and \code{"survival_tox_env_observed"} for
-#' the observed survival and \code{"sys_tox_observed"} and
-#' \code{"sys_tox_env_observed"} for the observed Sys. The default \code{NA}
-#' only plots the most important curves. Use \code{which = "all"} to display
-#' all curves. An empty vector or \code{NULL} creates just the axes.
+#' @param model The model object returned from \code{\link{ecxsys}}.
+#' @param which A vector of curve names to plot. Allowed are all values of
+#' \code{names(model$curves)} except \code{"concentration"}. See the
+#' \emph{Value} section of \code{\link{predict_ecxsys}} for descriptions of
+#' these names. Additionally, you can use \code{"survival_tox_observed"} and
+#' \code{"survival_tox_env_observed"} for the observed survival and
+#' \code{"sys_tox_observed"} and \code{"sys_tox_env_observed"} for the
+#' observed Sys. Use \code{"all"} to plot everything or \code{NA} to only draw
+#' the axis and labels. Invalid names will be silently ignored.
#'
#' @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_stress.R b/R/plot_stress.R
index f3dfd0b..4b027ea 100644
--- a/R/plot_stress.R
+++ b/R/plot_stress.R
@@ -20,7 +20,12 @@
#' @rdname plot_ecxsys
#' @export
plot_stress <- function(model,
- which = NA,
+ which = c(
+ "sys_tox",
+ "sys_tox_observed",
+ "sys_tox_env",
+ "sys_tox_env_observed"
+ ),
show_legend = FALSE,
xlab = "concentration",
ylab = "stress",
@@ -30,25 +35,15 @@ plot_stress <- function(model,
curve_names <- names(model$curves)
valid_names <- c(
curve_names[startsWith(curve_names, "stress") | startsWith(curve_names, "sys")],
- "sys_tox_observed", "sys_tox_env_observed" # the observed points
+ "sys_tox_observed"
)
- if (length(which) == 1 && is.na(which)) {
- which <- c("sys_tox", "sys_tox_observed")
- if (model$with_env) {
- which <- c(which, "sys_tox_env", "sys_tox_env_observed")
- }
- } else if ("all" %in% which) {
- if (length(which) > 1) {
- stop("'all' must not be combined with other curve names.")
- }
+ if (model$with_env) {
+ valid_names <- c(valid_names, "sys_tox_env_observed")
+ }
+ if ("all" %in% which) {
which <- valid_names
- } else if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
- warning("'which' contains names with 'env' but the model was built ",
- "without environmental stress.")
- which <- which[which %in% valid_names]
- } else if (any(!which %in% valid_names)) {
- warning("Argument 'which' contains invalid names.")
- which <- which[which %in% valid_names]
+ } else {
+ which <- intersect(which, valid_names)
}
curves <- model$curves
diff --git a/R/plot_survival.R b/R/plot_survival.R
index f99d9fb..7138bca 100644
--- a/R/plot_survival.R
+++ b/R/plot_survival.R
@@ -20,7 +20,14 @@
#' @rdname plot_ecxsys
#' @export
plot_survival <- function(model,
- which = NA,
+ which = c(
+ "survival_tox",
+ "survival_tox_sys",
+ "survival_tox_observed",
+ "survival_tox_env",
+ "survival_tox_env_sys",
+ "survival_tox_env_observed"
+ ),
show_legend = FALSE,
xlab = "concentration",
ylab = "survival",
@@ -30,26 +37,15 @@ plot_survival <- function(model,
curve_names <- names(model$curves)
valid_names <- c(
curve_names[startsWith(curve_names, "survival")],
- "survival_tox_observed", "survival_tox_env_observed" # observed points
+ "survival_tox_observed"
)
- if (length(which) == 1 && is.na(which)) {
- which <- c("survival_tox", "survival_tox_sys", "survival_tox_observed")
- if (model$with_env) {
- which <- c(which, "survival_tox_env", "survival_tox_env_sys",
- "survival_tox_env_observed")
- }
- } else if ("all" %in% which) {
- if (length(which) > 1) {
- stop("'all' must not be combined with other curve names.")
- }
+ if (model$with_env) {
+ valid_names <- c(valid_names, "survival_tox_env_observed")
+ }
+ if ("all" %in% which) {
which <- valid_names
- } else if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
- warning("'which' contains names with 'env' but the model was built ",
- "without environmental stress.")
- which <- which[which %in% valid_names]
- } else if (any(!which %in% valid_names)) {
- warning("Argument 'which' contains invalid names.")
- which <- which[which %in% valid_names]
+ } else {
+ which <- intersect(which, valid_names)
}
curves <- model$curves
diff --git a/man/plot_ecxsys.Rd b/man/plot_ecxsys.Rd
index ae35a65..1abfe99 100644
--- a/man/plot_ecxsys.Rd
+++ b/man/plot_ecxsys.Rd
@@ -9,7 +9,7 @@
\usage{
plot_stress(
model,
- which = NA,
+ which = c("sys_tox", "sys_tox_observed", "sys_tox_env", "sys_tox_env_observed"),
show_legend = FALSE,
xlab = "concentration",
ylab = "stress",
@@ -18,7 +18,8 @@ plot_stress(
plot_survival(
model,
- which = NA,
+ which = c("survival_tox", "survival_tox_sys", "survival_tox_observed",
+ "survival_tox_env", "survival_tox_env_sys", "survival_tox_env_observed"),
show_legend = FALSE,
xlab = "concentration",
ylab = "survival",
@@ -26,15 +27,16 @@ plot_survival(
)
}
\arguments{
-\item{model}{The object returned from \code{\link{ecxsys}}.}
+\item{model}{The model object returned from \code{\link{ecxsys}}.}
-\item{which}{A vector of names to plot. Allowed are the column names of the
-\code{model$curves} data frame. There is also
-\code{"survival_tox_observed"} and \code{"survival_tox_env_observed"} for
-the observed survival and \code{"sys_tox_observed"} and
-\code{"sys_tox_env_observed"} for the observed Sys. The default \code{NA}
-only plots the most important curves. Use \code{which = "all"} to display
-all curves. An empty vector or \code{NULL} creates just the axes.}
+\item{which}{A vector of curve names to plot. Allowed are all values of
+\code{names(model$curves)} except \code{"concentration"}. See the
+\emph{Value} section of \code{\link{predict_ecxsys}} for descriptions of
+these names. Additionally, you can use \code{"survival_tox_observed"} and
+\code{"survival_tox_env_observed"} for the observed survival and
+\code{"sys_tox_observed"} and \code{"sys_tox_env_observed"} for the
+observed Sys. Use \code{"all"} to plot everything or \code{NA} to only draw
+the axis and labels. Invalid names will be silently ignored.}
\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