From b847fec686bc1db59079412eb18063d3514ecf75 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 21 Dec 2016 10:35:16 +0100
Subject: TWA calculation for SFO, FOMC and DFOP (parent)
---
R/twa.R | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 65 insertions(+)
create mode 100644 R/twa.R
(limited to 'R')
diff --git a/R/twa.R b/R/twa.R
new file mode 100644
index 00000000..e8894b0b
--- /dev/null
+++ b/R/twa.R
@@ -0,0 +1,65 @@
+# Copyright (C) 2016 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+twa <- function(fit, windows) {
+ parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
+ obs_vars <- fit$obs_vars
+ if (length(obs_vars) > 1) {
+ warning("Calculation of maximum time weighted average concentrations is",
+ "currently only implemented for the parent compound using",
+ "analytical solutions")
+ }
+ obs_var <- obs_vars[1]
+ spec = fit$mkinmod$spec
+ type = spec[[1]]$type
+
+ M0 <- parms.all[paste0(obs_var, "_0")]
+
+ if (type == "SFO") {
+ k_name <- paste0("k_", obs_var)
+ if (fit$mkinmod$use_of_ff == "min") {
+ k_name <- paste0(k_name, "_sink")
+ }
+ k <- parms.all[k_name]
+ twafunc <- function(t) {
+ M0 * (1 - exp(- k * t)) / (k * t)
+ }
+ }
+ if (type == "FOMC") {
+ alpha <- parms.all["alpha"]
+ beta <- parms.all["beta"]
+ twafunc <- function(t) {
+ M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1)
+ }
+ }
+ if (type == "DFOP") {
+ k1 <- parms.all["k1"]
+ k2 <- parms.all["k2"]
+ g <- parms.all["g"]
+ twafunc <- function(t) {
+ M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t)))
+ }
+ }
+ if (type %in% c("HS", "IORE", "SFORB")) {
+ stop("Calculation of maximum time weighted average concentrations is currently ",
+ "not implemented for the ", type, " model.")
+ }
+ res <- twafunc(windows)
+ names(res) <- windows
+ return(res)
+}
--
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