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-rw-r--r--R/endpoints.R87
1 files changed, 38 insertions, 49 deletions
diff --git a/R/endpoints.R b/R/endpoints.R
index e4813db9..f1f47581 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -7,16 +7,22 @@
#' are equivalent to the rate constants 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}} or
-#' \code{\link{nlme.mmkin}}
+#' 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
+#'
+#' @param fit An object of class [mkinfit], [nlme.mmkin] or
+#' [saem.mmkin]. Or another object that has list components
+#' mkinmod containing an [mkinmod] degradation model, and two numeric vectors,
+#' bparms.optim and bparms.fixed, that contain parameter values
+#' for that model.
#' @importFrom stats optimize
#' @return A list with a matrix of dissipation times named distimes,
#' and, if applicable, a vector of formation fractions named ff
#' and, if the SFORB model was in use, a vector of eigenvalues
#' of these SFORB models, equivalent to DFOP rate constants
-#' @note The function is used internally by \code{\link{summary.mkinfit}}.
+#' @note The function is used internally by [summary.mkinfit],
+#' [summary.nlme.mmkin] and [summary.saem.mmkin].
#' @author Johannes Ranke
-#' @keywords manip
#' @examples
#'
#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
@@ -30,26 +36,9 @@
#'
#' @export
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
ep <- list()
- if (inherits(fit, "mkinfit")) {
- mkinmod <- fit$mkinmod
- parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
- } else {
- if (inherits(fit, "nlme.mmkin")) {
- mkinmod <- fit$mmkin_orig[[1]]$mkinmod
- bparms.optim <- backtransform_odeparms(fit$coefficients$fixed,
- mkinmod,
- transform_rates = fit$mmkin_orig[[1]]$transform_rates,
- transform_fractions = fit$mmkin_orig[[1]]$transform_fractions)
- parms.all <- c(bparms.optim, fit$bparms.fixed)
- } else {
- stop("Only implemented for mkinfit and nlme.mmkin objects")
- }
- }
+ mkinmod <- fit$mkinmod
+ degparms <- c(fit$bparms.optim, fit$bparms.fixed)
obs_vars <- names(mkinmod$spec)
ep$ff <- vector()
ep$SFORB <- vector()
@@ -61,9 +50,9 @@ endpoints <- function(fit) {
type = names(mkinmod$map[[obs_var]])[1]
# Get formation fractions if directly fitted, and calculate remaining fraction to sink
- f_names = grep(paste("^f", obs_var, sep = "_"), names(parms.all), value=TRUE)
+ f_names = grep(paste("^f", obs_var, sep = "_"), names(degparms), value=TRUE)
if (length(f_names) > 0) {
- f_values = parms.all[f_names]
+ f_values = degparms[f_names]
f_to_sink = 1 - sum(f_values)
names(f_to_sink) = ifelse(type == "SFORB",
paste(obs_var, "free", "sink", sep = "_"),
@@ -76,34 +65,34 @@ endpoints <- function(fit) {
# Get the rest
if (type == "SFO") {
- k_names = grep(paste("^k", obs_var, sep="_"), names(parms.all), value=TRUE)
- k_tot = sum(parms.all[k_names])
+ k_names = grep(paste("^k", obs_var, sep="_"), names(degparms), value=TRUE)
+ k_tot = sum(degparms[k_names])
DT50 = log(2)/k_tot
DT90 = log(10)/k_tot
if (mkinmod$use_of_ff == "min" && length(obs_vars) > 1) {
for (k_name in k_names)
{
- ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
+ ep$ff[[sub("k_", "", k_name)]] = degparms[[k_name]] / k_tot
}
}
}
if (type == "FOMC") {
- alpha = parms.all["alpha"]
- beta = parms.all["beta"]
+ alpha = degparms["alpha"]
+ beta = degparms["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$distimes[obs_var, c("DT50back")] = DT50_back
}
if (type == "IORE") {
- k_names = grep(paste("^k__iore", obs_var, sep="_"), names(parms.all), value=TRUE)
- k_tot = sum(parms.all[k_names])
+ k_names = grep(paste("^k__iore", obs_var, sep="_"), names(degparms), value=TRUE)
+ k_tot = sum(degparms[k_names])
# From the NAFTA kinetics guidance, p. 5
- n = parms.all[paste("N", obs_var, sep = "_")]
+ n = degparms[paste("N", obs_var, sep = "_")]
k = k_tot
# Use the initial concentration of the parent compound
source_name = mkinmod$map[[1]][[1]]
- c0 = parms.all[paste(source_name, "0", sep = "_")]
+ c0 = degparms[paste(source_name, "0", sep = "_")]
alpha = 1 / (n - 1)
beta = (c0^(1 - n))/(k * (n - 1))
DT50 = beta * (2^(1/alpha) - 1)
@@ -113,14 +102,14 @@ endpoints <- function(fit) {
if (mkinmod$use_of_ff == "min") {
for (k_name in k_names)
{
- ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
+ ep$ff[[sub("k_", "", k_name)]] = degparms[[k_name]] / k_tot
}
}
}
if (type == "DFOP") {
- k1 = parms.all["k1"]
- k2 = parms.all["k2"]
- g = parms.all["g"]
+ k1 = degparms["k1"]
+ k2 = degparms["k2"]
+ g = degparms["g"]
f <- function(log_t, x) {
t <- exp(log_t)
fraction <- g * exp( - k1 * t) + (1 - g) * exp( - k2 * t)
@@ -144,9 +133,9 @@ endpoints <- function(fit) {
ep$distimes[obs_var, c("DT50_k2")] = DT50_k2
}
if (type == "HS") {
- k1 = parms.all["k1"]
- k2 = parms.all["k2"]
- tb = parms.all["tb"]
+ k1 = degparms["k1"]
+ k2 = degparms["k2"]
+ tb = degparms["tb"]
DTx <- function(x) {
DTx.a <- (log(100/(100 - x)))/k1
DTx.b <- tb + (log(100/(100 - x)) - k1 * tb)/k2
@@ -165,11 +154,11 @@ endpoints <- function(fit) {
}
if (type == "SFORB") {
# FOCUS kinetics (2006), p. 60 f
- k_out_names = grep(paste("^k", obs_var, "free", sep="_"), names(parms.all), value=TRUE)
+ k_out_names = grep(paste("^k", obs_var, "free", sep="_"), names(degparms), value=TRUE)
k_out_names = setdiff(k_out_names, paste("k", obs_var, "free", "bound", sep="_"))
- k_1output = sum(parms.all[k_out_names])
- k_12 = parms.all[paste("k", obs_var, "free", "bound", sep="_")]
- k_21 = parms.all[paste("k", obs_var, "bound", "free", sep="_")]
+ k_1output = sum(degparms[k_out_names])
+ k_12 = degparms[paste("k", obs_var, "free", "bound", sep="_")]
+ k_21 = degparms[paste("k", obs_var, "bound", "free", sep="_")]
sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)
b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp
@@ -201,7 +190,7 @@ endpoints <- function(fit) {
for (k_out_name in k_out_names)
{
- ep$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
+ ep$ff[[sub("k_", "", k_out_name)]] = degparms[[k_out_name]] / k_1output
}
# Return the eigenvalues for comparison with DFOP rate constants
@@ -214,9 +203,9 @@ endpoints <- function(fit) {
}
if (type == "logistic") {
# FOCUS kinetics (2014) p. 67
- kmax = parms.all["kmax"]
- k0 = parms.all["k0"]
- r = parms.all["r"]
+ kmax = degparms["kmax"]
+ k0 = degparms["k0"]
+ r = degparms["r"]
DT50 = (1/r) * log(1 - ((kmax/k0) * (1 - 2^(r/kmax))))
DT90 = (1/r) * log(1 - ((kmax/k0) * (1 - 10^(r/kmax))))

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