diff --git a/DESCRIPTION b/DESCRIPTION
index 422ecaa2ca550bd37402085b183fab19ea0aa1be..b396809dd5850402898b79c47bdaf32ca5c4391a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: stressaddition
Type: Package
Title: Modeling Tri-Phasic Concentration-Response Relationships
-Version: 2.3.0
-Date: 2020-03-11
+Version: 2.4.0
+Date: 2020-03-13
Authors@R: c(person("Sebastian",
"Henz",
role = c("aut", "cre"),
@@ -31,4 +31,4 @@ Imports:
plotrix
Suggests:
testthat (>= 2.1.0)
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
diff --git a/NEWS.md b/NEWS.md
index 2b8b99f441931ee20633ddb96ff63ca1c671240e..f43297f4ed42b587536adf2677196cefe1837555 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,12 @@
+# 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.
+* Renamed `sys_tox_not_fitted` and `sys_tox_env_not_fitted` to `sys_tox_observed` and `sys_tox_env_observed` in the output of `ecxsys()`.
+
# stressaddition 2.3.0
* `predict_mixture()` accepts multiple values for the concentration of the second toxicant. Both concentration vectors must be the same length.
-* `predict_mixture()` returns a data frame with the concentrations and effects. Previously it was only a vector of effects.
+* `predict_mixture()` now returns a data frame with the concentrations and effects. Previously it was only a vector of effects.
* `predict_mixture()` received a new argument "effect_max" which scales the returned effect values.
* Renamed the arguments of `predict_mixture()` to use underscore letters a and b instad of 1 and 2. For example model_1 is now model_a.
diff --git a/R/ecxsys.R b/R/ecxsys.R
index d6ba1a7a4618efa91a3c32ed96bf5587487bda30..80e05b4f76b29e76b371c6c67dc628ba793b159c 100644
--- a/R/ecxsys.R
+++ b/R/ecxsys.R
@@ -234,7 +234,7 @@ ecxsys <- function(concentration,
hormesis_index,
original_options
)
- output$sys_tox_not_fitted <- fit_sys_output$sys[keep]
+ output$sys_tox_observed <- fit_sys_output$sys[keep]
output$sys_tox_mod <- fit_sys_output$sys_mod
if (inherits(fit_sys_output$sys_mod, "lm")) {
warning(
@@ -273,7 +273,7 @@ ecxsys <- function(concentration,
hormesis_index,
original_options
)
- output$sys_tox_env_not_fitted <- fit_sys_output$sys[keep]
+ output$sys_tox_env_observed <- fit_sys_output$sys[keep]
output$sys_tox_env_mod <- fit_sys_output$sys_mod
if (inherits(fit_sys_output$sys_mod, "lm")) {
warning(
diff --git a/R/plot_ecxsys.R b/R/plot_ecxsys.R
index 52a812ca66b4c61da63c89f5af78837130691d05..f1cd7ca72bf0006851b40ea7b726c556ed44e4ee 100644
--- a/R/plot_ecxsys.R
+++ b/R/plot_ecxsys.R
@@ -27,10 +27,13 @@
#' @name plot_ecxsys
#'
#' @param model The list returned from \code{\link{ecxsys}}.
-#' @param which A vector of curve names to plot. Allowed values are the column
-#' names of the \code{model$curves} data frame. The default \code{NULL} only
-#' plots the most important curves. Use \code{which = "all"} to display all
-#' curves.
+#' @param which A vector of names to plot. Allowed are the column names of the
+#' \code{model$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.
+#'
#' @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.
@@ -42,14 +45,18 @@
#' effect_tox_observed = c(90, 81, 92, 28, 0),
#' effect_tox_env_observed = c(29, 27, 33, 5, 0)
#' )
-#' plot_effect(model)
-#' plot_stress(model)
+#' plot_effect(model, show_legend = TRUE)
+#' plot_stress(model, show_legend = TRUE)
#'
#' # Plot all curves:
#' plot_effect(model, which = "all")
#' plot_stress(model, which = "all")
#'
#' # Plot only some selected curves:
-#' plot_effect(model, which = c("effect_tox", "effect_tox_env"))
-#' plot_stress(model, which = c("stress_tox", "stress_tox_env"))
+#' plot_effect(model, which = c("effect_tox_sys", "effect_tox_env_sys"))
+#' plot_stress(model, which = c("sys_tox", "sys_tox_env"))
+#'
+#' # Plot only the observed values:
+#' plot_effect(model, which = c("effect_tox_observed", "effect_tox_env_observed"))
+#' plot_stress(model, which = c("sys_tox_observed", "sys_tox_env_observed"))
NULL
diff --git a/R/plot_effect.R b/R/plot_effect.R
index 5a0da15f0b2de26ec4e4f6bd12fd31b8b5f8542b..0645f032b95d573703537f86a828064c80e33c2e 100644
--- a/R/plot_effect.R
+++ b/R/plot_effect.R
@@ -28,19 +28,22 @@ plot_effect <- function(model,
stopifnot(inherits(model, "ecxsys"))
curve_names <- names(model$curves)
- valid_names <- curve_names[startsWith(curve_names, "effect")]
+ valid_names <- c(
+ curve_names[startsWith(curve_names, "effect")],
+ "effect_tox_observed", "effect_tox_env_observed" # the observed points
+ )
if (is.null(which)) {
- which <- c("effect_tox", "effect_tox_sys")
+ which <- c("effect_tox", "effect_tox_sys", "effect_tox_observed")
if (model$with_env) {
- which <- c(which, "effect_tox_env", "effect_tox_env_sys")
+ which <- c(which, "effect_tox_env", "effect_tox_env_sys",
+ "effect_tox_env_observed")
}
} else if ("all" %in% which) {
- if (length(which) == 1) {
- which <- valid_names
- } else {
+ if (length(which) > 1) {
stop("'all' must not be combined with other curve names.")
}
- } else if (!all(which %in% valid_names)) {
+ which <- valid_names
+ } else if (any(!which %in% valid_names)) {
warning("Argument 'which' contains invalid names.")
if (!model$with_env && any(grepl("env", which, fixed = TRUE))) {
warning("'which' contains names with 'env' but the model was",
@@ -54,15 +57,6 @@ plot_effect <- function(model,
log_ticks <- get_log_ticks(curves$concentration)
concentration <- c(curves$concentration[1], model$args$concentration[-1])
- legend_df <- data.frame(
- text = character(),
- pch = numeric(),
- lty = numeric(),
- col = character(),
- order = numeric(), # controls sorting of legend elements
- stringsAsFactors = FALSE
- )
-
plot(
NA,
NA,
@@ -77,31 +71,22 @@ plot_effect <- function(model,
bty = "L"
)
- points(
- concentration,
- model$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) {
+ # 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_observed" %in% which) {
points(
concentration,
- model$args$effect_tox_env_observed,
+ model$args$effect_tox_observed,
pch = 16,
- col = "red"
+ col = "blue"
)
- 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(
@@ -110,7 +95,6 @@ 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(
@@ -119,16 +103,22 @@ plot_effect <- function(model,
col = "darkblue",
lty = 3
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox (LL5)", NA, 3, "darkblue", 3)
}
if (model$with_env) {
+ if ("effect_tox_env_observed" %in% which) {
+ points(
+ concentration,
+ model$args$effect_tox_env_observed,
+ pch = 16,
+ col = "red"
+ )
+ }
if ("effect_tox_env_sys" %in% which) {
lines(
curves$concentration,
curves$effect_tox_env_sys,
col = "red"
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox + env + sys", NA, 1, "red", 8)
}
if ("effect_tox_env" %in% which) {
lines(
@@ -137,7 +127,6 @@ plot_effect <- function(model,
col = "orange",
lty = 2
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox + env", NA, 2, "orange", 7)
}
if ("effect_tox_env_LL5" %in% which) {
lines(
@@ -146,7 +135,6 @@ plot_effect <- function(model,
col = "darkred",
lty = 3
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox + env (LL5)", NA, 3, "darkred", 6)
}
}
@@ -161,13 +149,28 @@ plot_effect <- function(model,
axis(2, col = NA, col.ticks = par("fg"), las = 1)
if (show_legend) {
- legend_df <- legend_df[order(legend_df$order), ]
- legend(
- "topright",
- legend = legend_df$text,
- pch = legend_df$pch,
- lty = legend_df$lty,
- col = legend_df$col
+ legend_df <- data.frame(
+ name = c("effect_tox_observed", "effect_tox", "effect_tox_sys",
+ "effect_tox_LL5", "effect_tox_env_observed",
+ "effect_tox_env", "effect_tox_env_sys", "effect_tox_env_LL5"),
+ text = c("tox (observed)", "tox", "tox + sys", "tox (LL5)",
+ "tox + env (observed)", "tox + env", "tox + env + sys",
+ "tox + env (LL5)"),
+ pch = c(16, NA, NA, NA, 16, NA, NA, NA),
+ lty = c(0, 2, 1, 3, 0, 2, 1, 3),
+ col = c("blue", "deepskyblue", "blue", "darkblue", "red", "orange",
+ "red", "darkred"),
+ stringsAsFactors = FALSE
)
+ legend_df <- legend_df[legend_df$name %in% which, ]
+ if (nrow(legend_df) > 0) {
+ legend(
+ "topright",
+ legend = legend_df$text,
+ pch = legend_df$pch,
+ lty = legend_df$lty,
+ col = legend_df$col
+ )
+ }
}
}
diff --git a/R/plot_stress.R b/R/plot_stress.R
index ee80cd49846519fae905291dd778af08b160c2c8..296f90a6b181cefe217f02aa56aebacacf4f4751 100644
--- a/R/plot_stress.R
+++ b/R/plot_stress.R
@@ -28,30 +28,27 @@ plot_stress <- function(model,
stopifnot(inherits(model, "ecxsys"))
curve_names <- names(model$curves)
- valid_names <- curve_names[
- startsWith(curve_names, "stress") | startsWith(curve_names, "sys")
- ]
+ valid_names <- c(
+ curve_names[startsWith(curve_names, "stress") | startsWith(curve_names, "sys")],
+ "sys_tox_observed", "sys_tox_env_observed" # the observed points
+ )
if (is.null(which)) {
- which <- c("sys_tox")
+ which <- c("sys_tox", "sys_tox_observed")
if (model$with_env) {
- which <- c(which, "sys_tox_env")
+ which <- c(which, "sys_tox_env", "sys_tox_env_observed")
}
} else if ("all" %in% which) {
- if (length(which) == 1) {
- which <- valid_names
- } else {
+ if (length(which) > 1) {
stop("'all' must not be combined with other curve names.")
}
- } else if (!all(which %in% valid_names)) {
+ which <- valid_names
+ } else if (any(!which %in% valid_names)) {
warning("Argument 'which' contains invalid names.")
if (!model$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]
- if (length(which) == 0) {
- stop("No curves to display.")
- }
}
temp <- adjust_plot_concentrations(model)
@@ -59,20 +56,14 @@ plot_stress <- function(model,
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
- )
+ curves_w <- curves[, which[!endsWith(which, "observed")]]
+ ymax <- if (NCOL(curves_w) == 0) 1 else max(curves_w, 1, na.rm = TRUE)
plot(
NA,
NA,
xlim = range(curves$concentration, na.rm = TRUE),
- ylim = c(0, max(curves[, which], 1, na.rm = TRUE)),
+ ylim = c(0, ymax),
log = "x",
xlab = xlab,
ylab = ylab,
@@ -84,13 +75,20 @@ plot_stress <- function(model,
# The lines are drawn in this order to ensure that dotted and dashed lines
# are on top of solid lines for better visibility.
+ if ("sys_tox_observed" %in% which) {
+ points(
+ concentration,
+ model$sys_tox_observed,
+ pch = 16,
+ col = "steelblue3"
+ )
+ }
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(
@@ -99,30 +97,29 @@ plot_stress <- function(model,
col = "deepskyblue",
lty = 2
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox", NA, 2, "deepskyblue", 1)
}
if ("sys_tox" %in% which) {
- points(
- concentration,
- model$sys_tox_not_fitted,
- pch = 16,
- col = "steelblue3"
- )
lines(
curves$concentration,
curves$sys_tox,
col = "steelblue3"
)
- legend_df[nrow(legend_df) + 1, ] <- list("sys (tox)", 16, 1, "steelblue3", 2)
}
if (model$with_env) {
+ if ("sys_tox_env_observed" %in% which) {
+ points(
+ concentration,
+ model$sys_tox_env_observed,
+ pch = 16,
+ col = "violetred"
+ )
+ }
if ("stress_tox_env_sys" %in% which) {
lines(
curves$concentration,
curves$stress_tox_env_sys,
col = "red"
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox + env + sys", NA, 1, "red", 7)
}
if ("stress_env" %in% which) {
lines(
@@ -131,7 +128,6 @@ plot_stress <- function(model,
col = "forestgreen",
lty = 3
)
- legend_df[nrow(legend_df) + 1, ] <- list("env", NA, 3, "forestgreen", 4)
}
if ("stress_tox_env" %in% which) {
lines(
@@ -140,21 +136,13 @@ plot_stress <- function(model,
col = "orange",
lty = 2
)
- legend_df[nrow(legend_df) + 1, ] <- list("tox + env", NA, 2, "orange", 5)
}
if ("sys_tox_env" %in% which) {
- points(
- concentration,
- model$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)
}
}
@@ -169,13 +157,28 @@ plot_stress <- function(model,
axis(2, col = NA, col.ticks = par("fg"), las = 1)
if (show_legend) {
- legend_df <- legend_df[order(legend_df$order), ]
- legend(
- "topright",
- legend = legend_df$text,
- pch = legend_df$pch,
- lty = legend_df$lty,
- col = legend_df$col
+ legend_df <- data.frame(
+ name = c( "sys_tox_observed", "stress_tox", "sys_tox",
+ "stress_tox_sys", "sys_tox_env_observed", "stress_env",
+ "stress_tox_env", "sys_tox_env", "stress_tox_env_sys"),
+ text = c("sys (tox, observed)", "tox", "sys (tox)", "tox + sys",
+ "sys (tox + env, observed)", "env", "tox + env",
+ "sys (tox + env)", "tox + env + sys"),
+ pch = c(16, NA, NA, NA, 16, NA, NA, NA, NA),
+ lty = c(0, 2, 1, 1, 0, 3, 2, 1, 1),
+ col = c("steelblue3", "deepskyblue", "steelblue3", "blue",
+ "violetred", "forestgreen", "orange", "violetred", "red"),
+ stringsAsFactors = FALSE
)
+ legend_df <- legend_df[legend_df$name %in% which, ]
+ if (nrow(legend_df) > 0) {
+ legend(
+ "topright",
+ 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 19d5c61ed5b184d8a9d0dd157f877806c3c8b0b5..1c9c32f9517e753c541357bc979485436dd6648a 100644
--- a/man/plot_ecxsys.Rd
+++ b/man/plot_ecxsys.Rd
@@ -27,10 +27,12 @@ plot_stress(
\arguments{
\item{model}{The list returned from \code{\link{ecxsys}}.}
-\item{which}{A vector of curve names to plot. Allowed values are the column
-names of the \code{model$curves} data frame. The default \code{NULL} only
-plots the most important curves. Use \code{which = "all"} to display all
-curves.}
+\item{which}{A vector of names to plot. Allowed are the column names of the
+\code{model$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.}
\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
@@ -48,14 +50,18 @@ model <- ecxsys(
effect_tox_observed = c(90, 81, 92, 28, 0),
effect_tox_env_observed = c(29, 27, 33, 5, 0)
)
-plot_effect(model)
-plot_stress(model)
+plot_effect(model, show_legend = TRUE)
+plot_stress(model, show_legend = TRUE)
# Plot all curves:
plot_effect(model, which = "all")
plot_stress(model, which = "all")
# Plot only some selected curves:
-plot_effect(model, which = c("effect_tox", "effect_tox_env"))
-plot_stress(model, which = c("stress_tox", "stress_tox_env"))
+plot_effect(model, which = c("effect_tox_sys", "effect_tox_env_sys"))
+plot_stress(model, which = c("sys_tox", "sys_tox_env"))
+
+# Plot only the observed values:
+plot_effect(model, which = c("effect_tox_observed", "effect_tox_env_observed"))
+plot_stress(model, which = c("sys_tox_observed", "sys_tox_env_observed"))
}
diff --git a/tests/testthat/test-ecxsys.R b/tests/testthat/test-ecxsys.R
index 01dcd29941a74c9616a370f3fd537601a2665b6f..d04e16f80ec3de4c862e7cde047edc5bfabda006 100644
--- a/tests/testthat/test-ecxsys.R
+++ b/tests/testthat/test-ecxsys.R
@@ -105,7 +105,7 @@ test_that("the discrete results have not changed", {
tolerance = 1e-4
)
expect_equal(
- mod$sys_tox_not_fitted,
+ mod$sys_tox_observed,
c(0.2541156, 0.2324304, 0, 0, 0),
tolerance = 1e-4
)
@@ -131,7 +131,7 @@ test_that("the discrete results have not changed", {
tolerance = 1e-4
)
expect_equal(
- mod$sys_tox_env_not_fitted,
+ mod$sys_tox_env_observed,
c(0.2566005, 0.1753250, 0, 0, 0),
tolerance = 1e-4
)