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

 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"), 

NEWS.md

+# 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.

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

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

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

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