Compiled models article, reduce distractions

- Added a section with platform specific notes on getting compiled
models to work to the compiled models article
- Don't return empty SFORB parameter list from endpoints() if there is no
SFORB model
- Avoid warnings when using standardized = TRUE in plot.mmkin()

1 files changed, 11 insertions, 9 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 14beadea..f7ee483a 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,12 +1,12 @@
 #' Function to calculate endpoints for further use from kinetic models fitted
 #' with mkinfit
-#' 
+#'
 #' This function calculates DT50 and DT90 values as well as formation fractions
 #' from kinetic models fitted with mkinfit. If the SFORB model was specified
 #' for one of the parents or metabolites, the Eigenvalues are returned. These
 #' are equivalent to the rate constantes of the DFOP model, but with the
 #' advantage that the SFORB model can also be used for metabolites.
-#' 
+#'
 #' @param fit An object of class \code{\link{mkinfit}}.
 #' @importFrom stats optimize
 #' @return A list with the components mentioned above.
@@ -14,10 +14,10 @@
 #' @author Johannes Ranke
 #' @keywords manip
 #' @examples
-#' 
+#'
 #'   fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-#'   endpoints(fit)  
-#' 
+#'   endpoints(fit)
+#'
 #' @export
 endpoints <- function(fit) {
   # Calculate dissipation times DT50 and DT90 and formation
@@ -29,8 +29,9 @@ endpoints <- function(fit) {
   parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
   ep$ff <- vector()
   ep$SFORB <- vector()
-  ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)),
-			    DT90 = rep(NA, length(obs_vars)),
+  ep$distimes <- data.frame(
+    DT50 = rep(NA, length(obs_vars)),
+    DT90 = rep(NA, length(obs_vars)),
     row.names = obs_vars)
   for (obs_var in obs_vars) {
     type = names(fit$mkinmod$map[[obs_var]])[1]
@@ -41,8 +42,8 @@ endpoints <- function(fit) {
       f_values = parms.all[f_names]
       f_to_sink = 1 - sum(f_values)
       names(f_to_sink) = ifelse(type == "SFORB",
-                              paste(obs_var, "free", "sink", sep = "_"),
-                              paste(obs_var, "sink", sep = "_"))
+        paste(obs_var, "free", "sink", sep = "_"),
+        paste(obs_var, "sink", sep = "_"))
       for (f_name in f_names) {
         ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]
       }
@@ -195,5 +196,6 @@ endpoints <- function(fit) {
     }
     ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)
   }
+  if (length(ep$SFORB) == 0) ep$SFORB <- NULL
   return(ep)
 }