dissect ecxsys()

That function is way too large. Dissect it into smaller functions. Create helper functions where possible.

Closes #5 (closed).

R/ec.R

@@ -8,11 +8,11 @@
 #' smallest concentration is returned.
 #'
 #' @param model This can be one of three types of objects: Either the output of
-#'   \code{ecxsys()} (object of class "ecxsys") or the output of a call to the
-#'   \code{fn} function in the ecxsys output or a data frame with a
-#'   "concentration" column and a \code{response_name} column. See the examples.
+#'   \code{\link{ecxsys}} or the output of \code{\link{predict_ecxsys}} or a
+#'   data frame with a "concentration" column and a \code{response_name} column.
+#'   See the examples.
 #' @param response_name The name of the effect or stress for which you want to
-#'   calculate the EC. Must be the name of a column in \code{model$curves}.
+#'   calculate the EC. Must be one of \code{colnames(model$curves)}.
 #' @param response_level The desired response level as a percentage between 0
 #'   and 100. For example with the value 10 the function will return the EC10,
 #'   i.e. the concentration where the response falls below 90 \% of the maximum
@@ -30,23 +30,21 @@
 #'     hormesis_concentration = 0.3
 #' )
 #'
-#' # using the ecxsys output directly:
-#' ec10_a <- ec(model, "effect_tox_sys", 10)
+#' # using the ecxsys() output or the curves therein directly:
+#' ec(model, "effect_tox_sys", 10)
+#' ec(model$curves, "effect_tox_sys", 10)
 #'
-#' # using predicted values:
-#' ec10_b <- ec(model$curves, "effect_tox_sys", 10)
-#'
-#' # using the output of fn():
+#' # using the output of predict_ecxsys() with custom concentrations:
 #' conc <- 10^seq(-9, 1, length.out = 1000)
-#' df_fn <- model$fn(conc)
-#' ec10_c <- ec(df_fn, "effect_tox_sys", 10)
+#' curves <- predict_ecxsys(model, conc)
+#' ec(curves, "effect_tox_sys", 10)
 #'
 #' # using a custom data frame:
 #' df_custom <- data.frame(
-#'     concentration = df_fn$concentration,
-#'     foo = df_fn$effect_tox_sys
+#'     concentration = curves$concentration,
+#'     foo = curves$effect_tox_sys
 #' )
-#' ec10_d <- ec(df_custom, "foo", 10)
+#' ec(df_custom, "foo", 10)
 #'
 #' @export
 ec <- function(model, response_name, response_level) {
@@ -62,7 +60,7 @@ ec <- function(model, response_name, response_level) {
         response_level < 100
     )
 
-    if (!inherits(model, c("ecxsys", "ecxsys_curves"))) {
+    if (!inherits(model, c("ecxsys", "ecxsys_predicted"))) {
         if (is.data.frame(model)) {
             concentration <- model$concentration
             response <- model[, response_name]
@@ -72,7 +70,7 @@ ec <- function(model, response_name, response_level) {
     } else if (inherits(model, "ecxsys")) {
         concentration <- model$curves$concentration
         response <- model$curves[, response_name]
-    } else if (inherits(model, "ecxsys_curves")) {
+    } else if (inherits(model, "ecxsys_predicted")) {
         concentration <- model$concentration
         response <- model[, response_name]
     }