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authorJohannes Ranke <jranke@uni-bremen.de>2017-01-19 10:36:19 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-19 10:36:19 +0100
commitdd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 (patch)
treea954197c4e8e093d4b08c08eab14753b58602ff4 /R
parent3ead7acba845b4f2552f555dfb29da889ed0cda8 (diff)
Move mkin::twa to pfm::max_twa.mkinfit
- Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but never released with it - Add a test to check max_twa.one_box() against analytical solutions in max_twa.mkinfit(). - Clean up R CMD check - Update docs
Diffstat (limited to 'R')
-rw-r--r--R/twa.R88
1 files changed, 81 insertions, 7 deletions
diff --git a/R/twa.R b/R/twa.R
index fcf49c0..88cfec3 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2017 Johannes Ranke
+# Copyright (C) 2016,2017 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package pfm
@@ -23,6 +23,7 @@
#'
#' @param x When numeric, this is the half-life to be used for an exponential
#' decline. If x is an mkinfit object, the decline is calculated from this object
+#' @param ini The initial amount for each compound
#' @param t_end End of the time series
#' @param res Resolution of the time series
#' @param ... Further arguments passed to methods
@@ -44,7 +45,7 @@
#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#' pred_2 <- one_box(fit_2)
#' plot(pred_2)
-one_box <- function(x, ...,
+one_box <- function(x, ini, ...,
t_end = 100, res = 0.01)
{
UseMethod("one_box")
@@ -52,7 +53,7 @@ one_box <- function(x, ...,
#' @rdname one_box
#' @export
-one_box.numeric <- function(x, ...,
+one_box.numeric <- function(x, ini = 1, ...,
t_end = 100, res = 0.01)
{
half_life = x
@@ -68,7 +69,7 @@ one_box.numeric <- function(x, ...,
#' @rdname one_box
#' @param parms A named numeric vector containing the model parameters
#' @export
-one_box.character <- function(x, parms, ...,
+one_box.character <- function(x, ini = 1, parms, ...,
t_end = 100, res = 0.01)
{
parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE")
@@ -96,11 +97,18 @@ one_box.character <- function(x, parms, ...,
#' @rdname one_box
#' @importFrom mkin mkinpredict
#' @export
-one_box.mkinfit <- function(x, ..., t_end = 100, res = 0.01) {
+one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01) {
fit <- x
+
+ ini = match.arg(ini)
+ if (ini == "model") {
+ odeini = x$bparms.state
+ } else {
+ odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1))
+ names(odeini) <- names(fit$mkinmod$spec)
+ }
+
t_out = seq(0, t_end, by = res)
- odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1))
- names(odeini) <- names(fit$mkinmod$spec)
if (length(fit$mkinmod$spec) == 1) solution_type = "analytical"
else solution_type = "deSolve"
@@ -216,6 +224,7 @@ sawtooth <- function(x, n = 1, i = 365,
#' @param x An object of type \code{\link{one_box}}
#' @param window The size of the moving window
#' @seealso \code{\link{max_twa}}
+#' @importFrom stats start end
#' @export
#' @examples
#' pred <- sawtooth(one_box(10),
@@ -247,12 +256,77 @@ twa.one_box <- function(x, window = 21)
#' for finding the maximum. It is therefore recommended to check this using
#' \code{\link{plot.one_box}} using the window size for the argument
#' \code{max_twa}.
+#'
+#' The method working directly on fitted \code{\link{mkinfit}} objects uses the
+#' equations given in the PEC soil section of the FOCUS guidance and is restricted
+#' SFO, FOMC and DFOP models and to the parent compound
+#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+#' Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+#' Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
#' @seealso \code{\link{twa}}
#' @inheritParams twa
#' @export
+#' @examples
+#' pred <- sawtooth(one_box(10),
+#' applications = data.frame(time = c(0, 7), amount = c(1, 1)))
+#' max_twa(pred)
+#' pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+#' max_twa(pred_FOMC)
max_twa <- function(x, window = 21) UseMethod("max_twa")
#' @export
+max_twa.mkinfit <- function(x, window = 21) {
+ fit <- x
+ parms.all <- c(fit$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(t = window)
+ names(res) <- window
+ return(res)
+}
+
+#' @export
max_twa.one_box <- function(x, window = 21)
{
freq = frequency(x)

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