diff options
Diffstat (limited to 'R/endpoints.R')
| -rw-r--r-- | R/endpoints.R | 28 |
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"]
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