Nearly complete support for IORE, pending mkinerrmin

1 files changed, 25 insertions, 3 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 676831a0..ae9aa3ec 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,11 +1,11 @@
 endpoints <- function(fit) {

   # 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 any SFORB models

+  # 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 any SFORB models

   ep <- list()

   obs_vars <- fit$obs_vars

-  parms.all <- fit$bparms.ode

+  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)), 

@@ -49,6 +49,28 @@ endpoints <- function(fit) {
       DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011

       ep$distimes[obs_var, c("DT50back")] = DT50_back

     }

+    if (type == "IORE") {

+      k_names = grep(paste("k.iore", obs_var, sep="_"), names(parms.all), value=TRUE)

+      k_tot = sum(parms.all[k_names])

+      # From the NAFTA kinetics guidance, p. 5

+      n = parms.all[paste("N", obs_var, sep = "_")]

+      k = k_tot

+      # Use the initial concentration of the parent compound

+      source_name = fit$mkinmod$map[[1]][[1]]

+      c0 = parms.all[paste(source_name, "0", sep = "_")]

+      alpha = 1 / (n - 1)

+      beta = (c0^(1 - n))/(k * (n - 1))

+      DT50 = beta * (2^(1/alpha) - 1)

+      DT90 = beta * (10^(1/alpha) - 1)

+      DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011

+      ep$distimes[obs_var, c("DT50back")] = DT50_back

+      if (fit$mkinmod$use_of_ff == "min") {

+        for (k_name in k_names)

+        {

+          ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot

+        }

+      }

+    }

     if (type == "DFOP") {

       k1 = parms.all["k1"]

       k2 = parms.all["k2"]