diff --git a/NEWS.md b/NEWS.md
index 21adea503dc8fa4e56ec37900e266b814ea88ee5..3f905ce7e4d2881a6a6cd4f86d18d0e8a49b9a16 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,10 @@
# stressaddition (development version)
-* Added predict_mixture() for the prediction of the effects of mixtures of two toxicants.
-* Fixed documentation of `ecxsys()` and `predict_ecxsys`.
+* The functions `plot_effect()` and `plot_stress()` gain a `which` argument that controls which curves are plotted. Consequently, the `show_LL5_model` argument of `plot_effect()` was removed.
+* Added arguments `xlab` and `ylab` to `plot_stress`.
+* Changed some colors of the stress curves so they better match with the colors of related effect curves.
+* Added `predict_mixture()` for the prediction of the effects of mixtures of two toxicants.
+* Fixed documentation of `ecxsys()` and `predict_ecxsys()`.
# stressaddition 2.0.0
diff --git a/R/helpers.R b/R/helpers.R
index f13f0d09f1c7da52f091e498dda5960e0bb3ea95..1b9fea35ab1ac236d2b0d9d296a7d483263247dd 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -33,12 +33,12 @@ get_log_ticks <- function(x) {
}
-adjust_smooth_concentrations <- function(curves, conc_adjust_factor) {
+adjust_smooth_concentrations <- function(model) {
# Helper for the plot functions, not exported.
# Deals with the concentrations which are unnecessary for plotting.
# This means it removes the concentrations in the gap and scales the
# concentrations left of the gap up.
-
+ curves <- model$curves
gap_idx <- min(which(!curves$use_for_plotting))
# Keep only the values to the left and right of the axis break:
@@ -50,7 +50,7 @@ adjust_smooth_concentrations <- function(curves, conc_adjust_factor) {
# Shift the small concentrations upwards so the plot has a nice x-axis:
curves$concentration[1:gap_idx] <-
- curves$concentration[1:gap_idx] / conc_adjust_factor
+ curves$concentration[1:gap_idx] / model$conc_adjust_factor
list(
curves = curves,
diff --git a/R/plot_ecxsys.R b/R/plot_ecxsys.R
index 0ea5e493068b8d9d98eb359c181b357f546ef6ea..42ee2857c4b66187733c6af19afa9c813dbcaef6 100644
--- a/R/plot_ecxsys.R
+++ b/R/plot_ecxsys.R
@@ -3,16 +3,18 @@
#' Plot the results of the ECx-SyS model
#'
-#' Convenience functions to plot the observed and modeled effect and the
-#' system stress with and without environmental stress.
+#' Plot the observed and modeled effects and stresses.
#'
#' @name plot_ecxsys
#'
#' @param model The list returned from \code{\link{ecxsys}}.
-#' @param show_LL5_model Should the log-logistic models be plotted for
-#' comparison? Defaults to \code{FALSE}.
-#' @param show_legend Should the plot include a legend? Defaults to FALSE
-#' because it may cover some points or lines depending on the plot size.
+#' @param which A vector of curve names to plot. Allowed values are the column
+#' names of the \code{model$curves} data frame. The default \code{NULL} only
+#' plots the most important curves. Use \code{which = "all"} to display all
+#' curves.
+#' @param show_legend Should the plot include a legend? Defaults to \code{FALSE}
+#' because it may cover some parts of the plot depending on the plot size and
+#' the number of elements shown.
#' @param xlab,ylab Axis labels.
#'
#' @examples model <- ecxsys(
@@ -23,4 +25,8 @@
#' )
#' plot_effect(model)
#' plot_stress(model)
+#'
+#' # Plot all curves:
+#' plot_effect(model, which = "all")
+#' plot_stress(model, which = "all")
NULL
diff --git a/R/plot_effect.R b/R/plot_effect.R
index b4fd9418853fcc63ab893dc006fa79564221318f..b3d19c80b9cb0e4a20259092f847e8db5d31db93 100644
--- a/R/plot_effect.R
+++ b/R/plot_effect.R
@@ -2,33 +2,47 @@
#' @export
plot_effect <- function(model,
which = NULL,
- show_observed = TRUE,
show_legend = FALSE,
xlab = "concentration",
ylab = "effect") {
stopifnot(inherits(model, "ecxsys"))
+
curve_names <- names(model$curves)
valid_names <- curve_names[startsWith(curve_names, "effect")]
if (is.null(which)) {
- which <- c("effect_tox_sys", "effect_tox_env_sys")
- } else if (length(which) == 1 && which == "all") {
- which <- valid_names
+ which <- c("effect_tox_sys")
+ if (model$with_env) {
+ which <- c(which, "effect_tox_env_sys")
+ }
+ } else if ("all" %in% which) {
+ if (length(which) == 1) {
+ which <- valid_names
+ } else {
+ stop("'all' must not be combined with other curve names.")
+ }
} else if (!all(which %in% valid_names)) {
- stop("Argument 'which' contains invalid names. Only effects are allowed.")
- }
- if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
- warning("'which' contains names with 'env' but the model was built ",
- "without environmental effects.")
+ warning("Argument 'which' contains invalid names.")
+ if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
+ warning("'which' contains names with 'env' but the model was",
+ " built without environmental effects.")
+ }
+ which <- which[which %in% valid_names]
}
- temp <- adjust_smooth_concentrations(
- model$curves,
- model$conc_adjust_factor
- )
+ temp <- adjust_smooth_concentrations(model)
curves <- temp$curves
log_ticks <- get_log_ticks(curves$concentration)
concentration <- c(curves$concentration[1], model$args$concentration[-1])
+ legend_df <- data.frame(
+ text = character(),
+ pch = numeric(),
+ lty = numeric(),
+ col = character(),
+ order = numeric(), # controls sorting of legend elements
+ stringsAsFactors = FALSE
+ )
+
plot(
NA,
NA,
@@ -42,37 +56,31 @@ plot_effect <- function(model,
las = 1
)
- if (show_observed) {
+ points(
+ concentration,
+ model$args$effect_tox_observed,
+ pch = 16,
+ col = "blue"
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox (observed)", 16, 0, "blue", 1)
+ if (model$with_env) {
points(
concentration,
- model$args$effect_tox_observed,
+ model$args$effect_tox_env_observed,
pch = 16,
- col = "blue"
- )
- if (model$with_env) {
- points(
- concentration,
- model$args$effect_tox_env_observed,
- pch = 16,
- col = "red"
- )
- }
- }
- if ("effect_tox_LL5" %in% which) {
- lines(
- curves$concentration,
- curves$effect_tox_LL5,
- col = "darkblue",
- lty = 4
+ col = "red"
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env (observed)", 16, 0, "red", 2)
}
-
+ # The lines are drawn in this order to ensure that dotted and dashed lines
+ # are on top of solid lines for better visibility.
if ("effect_tox_sys" %in% which) {
lines(
curves$concentration,
curves$effect_tox_sys,
col = "blue"
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + sys", NA, 1, "blue", 5)
}
if ("effect_tox" %in% which) {
lines(
@@ -81,22 +89,25 @@ plot_effect <- function(model,
col = "deepskyblue",
lty = 2
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox", NA, 2, "deepskyblue", 4)
+ }
+ if ("effect_tox_LL5" %in% which) {
+ lines(
+ curves$concentration,
+ curves$effect_tox_LL5,
+ col = "darkblue",
+ lty = 3
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox (LL5)", NA, 3, "darkblue", 3)
}
if (model$with_env) {
- if ("effect_tox_env_LL5" %in% which) {
- lines(
- curves$concentration,
- curves$effect_tox_env_LL5,
- col = "darkred",
- lty = 4
- )
- }
if ("effect_tox_env_sys" %in% which) {
lines(
curves$concentration,
curves$effect_tox_env_sys,
col = "red"
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env + sys", NA, 1, "red", 8)
}
if ("effect_tox_env" %in% which) {
lines(
@@ -105,6 +116,16 @@ plot_effect <- function(model,
col = "orange",
lty = 2
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env", NA, 2, "orange", 7)
+ }
+ if ("effect_tox_env_LL5" %in% which) {
+ lines(
+ curves$concentration,
+ curves$effect_tox_env_LL5,
+ col = "darkred",
+ lty = 3
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env (LL5)", NA, 3, "darkred", 6)
}
}
@@ -113,28 +134,13 @@ plot_effect <- function(model,
plotrix::axis.break(1, breakpos = temp$axis_break_conc)
if (show_legend) {
- legend_text <- c("tox", "tox + sys")
- legend_pch <- c(NA, 16)
- legend_lty <- c(2, 1)
- legend_col <- c("deepskyblue", "blue")
- if (model$with_env) {
- legend_text <- c(legend_text, "tox + env", "tox + env + sys")
- legend_pch <- c(legend_pch, NA, 16)
- legend_lty <- c(legend_lty, 2, 1)
- legend_col <- c(legend_col, "orange", "red")
- }
- if (show_LL5_model) {
- legend_text <- c(legend_text, "tox (LL5)", "tox + env (LL5)")
- legend_pch <- c(legend_pch, NA, NA)
- legend_lty <- c(legend_lty, 4, 4)
- legend_col <- c(legend_col, "darkblue", "darkred")
- }
+ legend_df <- legend_df[order(legend_df$order), ]
legend(
"topright",
- legend = legend_text,
- pch = legend_pch,
- lty = legend_lty,
- col = legend_col
+ legend = legend_df$text,
+ pch = legend_df$pch,
+ lty = legend_df$lty,
+ col = legend_df$col
)
}
}
diff --git a/R/plot_stress.R b/R/plot_stress.R
index cccdcbcb0e7176262087fa331d74806514e90c63..c48c978d34260ed1e0cd037088194cf49b3027a7 100644
--- a/R/plot_stress.R
+++ b/R/plot_stress.R
@@ -1,53 +1,141 @@
#' @rdname plot_ecxsys
#' @export
-plot_stress <- function(model, show_legend = FALSE) {
+plot_stress <- function(model,
+ which = NULL,
+ show_legend = FALSE,
+ xlab = "concentration",
+ ylab = "stress") {
stopifnot(inherits(model, "ecxsys"))
- temp <- adjust_smooth_concentrations(
- model$curves,
- model$conc_adjust_factor
- )
+
+ curve_names <- names(model$curves)
+ valid_names <- curve_names[
+ startsWith(curve_names, "stress") | startsWith(curve_names, "sys")
+ ]
+ if (is.null(which)) {
+ which <- c("sys_tox")
+ if (model$with_env) {
+ which <- c(which, "sys_tox_env")
+ }
+ } else if ("all" %in% which) {
+ if (length(which) == 1) {
+ which <- valid_names
+ } else {
+ stop("'all' must not be combined with other curve names.")
+ }
+ } else if (!all(which %in% valid_names)) {
+ warning("Argument 'which' contains invalid names.")
+ if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
+ warning("'which' contains names with 'env' but the model was",
+ " built without environmental effects.")
+ }
+ which <- which[which %in% valid_names]
+ if (length(which) == 0) {
+ stop("No curves to display.")
+ }
+ }
+
+ temp <- adjust_smooth_concentrations(model)
curves <- temp$curves
axis_break_conc <- temp$axis_break_conc
log_ticks <- get_log_ticks(curves$concentration)
concentration <- c(curves$concentration[1], model$args$concentration[-1])
+ legend_df <- data.frame(
+ text = character(),
+ pch = numeric(),
+ lty = numeric(),
+ col = character(),
+ order = numeric(), # controls sorting of legend elements
+ stringsAsFactors = FALSE
+ )
+
plot(
NA,
NA,
xlim = range(curves$concentration, na.rm = TRUE),
- ylim = c(0, 1),
+ ylim = c(0, max(curves[, which], 1, na.rm = TRUE)),
log = "x",
- xlab = "concentration",
- ylab = "system stress",
+ xlab = xlab,
+ ylab = ylab,
xaxt = "n",
las = 1,
bty = "L"
)
- lines(
- curves$concentration,
- curves$sys_tox,
- col = "blue"
- )
- points(
- concentration,
- model$sys_tox_not_fitted,
- pch = 16,
- col = "blue"
- )
-
- if (model$with_env) {
+ # The lines are drawn in this order to ensure that dotted and dashed lines
+ # are on top of solid lines for better visibility.
+ if ("stress_tox_sys" %in% which) {
+ lines(
+ curves$concentration,
+ curves$stress_tox_sys,
+ col = "blue"
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + sys", NA, 1, "blue", 3)
+ }
+ if ("stress_tox" %in% which) {
lines(
curves$concentration,
- curves$sys_tox_env,
- col = "red"
+ curves$stress_tox,
+ col = "deepskyblue",
+ lty = 2
)
+ legend_df[nrow(legend_df) + 1, ] <- list("tox", NA, 2, "deepskyblue", 1)
+ }
+ if ("sys_tox" %in% which) {
points(
concentration,
- model$sys_tox_env_not_fitted,
+ model$sys_tox_not_fitted,
pch = 16,
- col = "red"
+ col = "steelblue3"
)
+ lines(
+ curves$concentration,
+ curves$sys_tox,
+ col = "steelblue3"
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("sys (tox)", 16, 1, "steelblue3", 2)
+ }
+ if (model$with_env) {
+ if ("stress_tox_env_sys" %in% which) {
+ lines(
+ curves$concentration,
+ curves$stress_tox_env_sys,
+ col = "red"
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env + sys", NA, 1, "red", 7)
+ }
+ if ("stress_env" %in% which) {
+ lines(
+ curves$concentration,
+ curves$stress_env,
+ col = "forestgreen",
+ lty = 3
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("env", NA, 3, "forestgreen", 4)
+ }
+ if ("stress_tox_env" %in% which) {
+ lines(
+ curves$concentration,
+ curves$stress_tox_env,
+ col = "orange",
+ lty = 2
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("tox + env", NA, 2, "orange", 5)
+ }
+ if ("sys_tox_env" %in% which) {
+ points(
+ concentration,
+ model$sys_tox_env_not_fitted,
+ pch = 16,
+ col = "violetred"
+ )
+ lines(
+ curves$concentration,
+ curves$sys_tox_env,
+ col = "violetred"
+ )
+ legend_df[nrow(legend_df) + 1, ] <- list("sys (tox + env)", 16, 1, "violetred", 6)
+ }
}
axis(1, at = log_ticks$major, labels = log_ticks$major_labels)
@@ -55,18 +143,13 @@ plot_stress <- function(model, show_legend = FALSE) {
plotrix::axis.break(1, breakpos = axis_break_conc)
if (show_legend) {
- legend_text <- c("tox")
- legend_col <- c("blue")
- if (model$with_env) {
- legend_text <- c(legend_text, "tox + env")
- legend_col <- c(legend_col, "red")
- }
+ legend_df <- legend_df[order(legend_df$order), ]
legend(
"topright",
- legend = legend_text,
- col = legend_col,
- pch = 16,
- lty = 1
+ legend = legend_df$text,
+ pch = legend_df$pch,
+ lty = legend_df$lty,
+ col = legend_df$col
)
}
}
diff --git a/man/plot_ecxsys.Rd b/man/plot_ecxsys.Rd
index 7e7252d4281051aa90d592a714e0bcb9e09bb551..2d401ca4c6ba12818bdbc0e0b3ee1224f35b2785 100644
--- a/man/plot_ecxsys.Rd
+++ b/man/plot_ecxsys.Rd
@@ -10,7 +10,7 @@ plot_effect(
model,
which = NULL,
show_observed = TRUE,
- show_legend = FALSE,
+ show_legend = TRUE,
xlab = "concentration",
ylab = "effect"
)
@@ -20,17 +20,20 @@ plot_stress(model, show_legend = FALSE)
\arguments{
\item{model}{The list returned from \code{\link{ecxsys}}.}
-\item{show_legend}{Should the plot include a legend? Defaults to FALSE
-because it may cover some points or lines depending on the plot size.}
+\item{which}{A vector of curve names to plot. Allowed values are the column
+names of the \code{model$curves} data frame. The default \code{NULL} only
+plots the most important curves. Use \code{which = "all"} to display all
+curves.}
-\item{xlab, ylab}{Axis labels.}
+\item{show_observed}{Should the observed values be plotted as points?}
+
+\item{show_legend}{Should the plot include a legend? May cover some parts of
+the plot depending on the plot size and the number of elements shown.}
-\item{show_LL5_model}{Should the log-logistic models be plotted for
-comparison? Defaults to \code{FALSE}.}
+\item{xlab, ylab}{Axis labels.}
}
\description{
-Convenience functions to plot the observed and modeled effect and the
-system stress with and without environmental stress.
+Plot the observed and modeled effects and stresses.
}
\examples{
model <- ecxsys(
@@ -41,4 +44,8 @@ model <- ecxsys(
)
plot_effect(model)
plot_stress(model)
+
+# Plot all curves:
+plot_effect(model, which = "all")
+plot_stress(model, which = "all")
}