Support formation fractions without sink pathway, updates

1 files changed, 13 insertions, 11 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index a5bebd71..676831a0 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,8 +1,8 @@
 endpoints <- function(fit) {

-  # Calculate dissipation times DT50 and DT90 and, if necessary, formation

-  # fractions and SFORB eigenvalues from optimised parameters

+  # Calculate dissipation times DT50 and DT90 and formation

+  # fractions as well as SFORB eigenvalues from optimised parameters

   # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP,

-  # as well as from Eigenvalues b1 and b2 of the SFORB model

+  # as well as from Eigenvalues b1 and b2 of any SFORB models

   ep <- list()

   obs_vars <- fit$obs_vars

   parms.all <- fit$bparms.ode

@@ -16,15 +16,17 @@ endpoints <- function(fit) {
 

     # Get formation fractions if directly fitted, and calculate remaining fraction to sink

     f_names = grep(paste("f", obs_var, sep = "_"), names(parms.all), value=TRUE)

-    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 = "_"))

-    for (f_name in f_names) {

-      ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]

+    if (length(f_names) > 0) {

+      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 = "_"))

+      for (f_name in f_names) {

+        ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]

+      }

+      ep$ff = append(ep$ff, f_to_sink)

     }

-    ep$ff = append(ep$ff, f_to_sink)

 

     # Get the rest

     if (type == "SFO") {