aboutsummaryrefslogtreecommitdiff
path: root/R
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2014-06-26 11:36:02 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-06-26 11:36:02 +0200
commita7e6b9f9a0ba46f84929603296d3dd4a0cbe4787 (patch)
treecb4b810c984e8b9ea0f8f85689a2adfe88509796 /R
parente8cf8558b7d071f800a65c3688f19d5ae400c33f (diff)
Calculate additional DT50 values for non-SFO models
Diffstat (limited to 'R')
-rw-r--r--R/endpoints.R22
1 files changed, 20 insertions, 2 deletions
diff --git a/R/endpoints.R b/R/endpoints.R
index c9a6a51f..18d8159b 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,6 +1,8 @@
-endpoints <- function(fit, pseudoDT50 = FALSE) {
+endpoints <- function(fit) {
# Calculate dissipation times DT50 and DT90 and, if necessary, formation
# fractions and 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
ep <- list()
obs_vars <- fit$obs_vars
parms.all <- fit$bparms.ode
@@ -40,6 +42,8 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
beta = parms.all["beta"]
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$distimes[obs_var, c("DT50back")] = DT50_back
}
if (type == "DFOP") {
k1 = parms.all["k1"]
@@ -54,6 +58,10 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
DT50 = ifelse(DTmax - DT50.o < 0.1, NA, DT50.o)
DT90.o <- optimize(f, c(0.001, DTmax), x=90)$minimum
DT90 = ifelse(DTmax - DT90.o < 0.1, NA, DT90.o)
+ DT50_k1 = log(2)/k1
+ DT50_k2 = log(2)/k2
+ ep$distimes[obs_var, c("DT50_k1")] = DT50_k1
+ ep$distimes[obs_var, c("DT50_k2")] = DT50_k2
}
if (type == "HS") {
k1 = parms.all["k1"]
@@ -68,6 +76,10 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
}
DT50 <- DTx(50)
DT90 <- DTx(90)
+ DT50_k1 = log(2)/k1
+ DT50_k2 = log(2)/k2
+ ep$distimes[obs_var, c("DT50_k1")] = DT50_k1
+ ep$distimes[obs_var, c("DT50_k2")] = DT50_k2
}
if (type == "SFORB") {
# FOCUS kinetics (2006), p. 60 f
@@ -98,11 +110,17 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
ep$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
}
+ DT50_b1 = log(2)/b1
+ DT50_b2 = log(2)/b2
+
# Return the eigenvalues for comparison with DFOP rate constants
ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
+
+ ep$distimes[obs_var, c("DT50_b1")] = DT50_b1
+ ep$distimes[obs_var, c("DT50_b2")] = DT50_b2
}
- ep$distimes[obs_var, ] = c(DT50, DT90)
+ ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)
}
return(ep)
}

Contact - Imprint