Add facilities to calculate decline curves

8 files changed, 208 insertions, 1 deletions

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 98e9142..4c41019 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -7,7 +7,7 @@ Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"))
 Description: Utilities for simple PEC calculations and for dealing with data
   from some FOCUS pesticide fate modelling software.
-Depends: R6
+Depends: R6, mkin
 Suggests: testthat
 License: GPL
 LazyLoad: yes
diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 00b0022..2d95da4 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -3,7 +3,11 @@
 S3method(plot,TOXSWA_cwa)
 export(PEC_soil)
 export(PEC_sw_drift)
+export(PEC_sw_drift_ini)
+export(SFO_actual_twa)
 export(TOXSWA_cwa)
 export(geomean)
+export(pfm_degradation)
 export(read.TOXSWA_cwa)
+import(mkin)
 importFrom(R6,R6Class)
diff --git a/pkg/R/SFO_actual_twa.R b/pkg/R/SFO_actual_twa.R
new file mode 100644
index 0000000..7facb6a
--- /dev/null
+++ b/pkg/R/SFO_actual_twa.R
@@ -0,0 +1,36 @@
+# Copyright (C) 2015  Johannes Ranke
+# Contact: jranke@uni-bremen.de
+# This file is part of the R package pfm
+
+# This program 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/>
+
+#' Actual and maximum moving window time average concentrations for SFO kinetics
+#'
+#' @param DT50 The half-life.
+#' @param times The output times, and window sizes for time weighted average concentrations
+#' @export
+#' @author Johannes Ranke
+#' @source FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+#'   Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, 
+#'   18 December 2014, p. 251
+#' @examples
+#' SFO_actual_twa(10)
+SFO_actual_twa <- function(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
+{
+  k = log(2)/DT50
+  result <- data.frame(actual = 1 * exp(-k * times),
+                       twa = (1 - exp(-k * times))/(k * times),
+                       row.names = times)
+  return(result)
+}
diff --git a/pkg/R/pfm_degradation.R b/pkg/R/pfm_degradation.R
new file mode 100644
index 0000000..d1d2f9d
--- /dev/null
+++ b/pkg/R/pfm_degradation.R
@@ -0,0 +1,48 @@
+# Copyright (C) 2015  Johannes Ranke
+# Contact: jranke@uni-bremen.de
+# This file is part of the R package pfm
+
+# This program 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/>
+
+#' Calculate a time course of relative concentrations based on an mkinmod model
+#'
+#' @import mkin
+#' @param model The degradation model to be used. Either a parent only model like
+#'   'SFO' or 'FOMC', or an mkinmod object
+#' @param DT50 The half-life. This is only used when simple exponential decline
+#'   is calculated (SFO model).
+#' @param parms The parameters used for the degradation model
+#' @param years For how many years should the degradation be predicted?
+#' @param step_days What step size in days should the output have?
+#' @param times The output times
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' pfm_degradation("SFO", DT50 = 10)
+pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50),
+                            years = 1, step_days = 1,
+                            times = seq(0, years * 365, by = step_days))
+{
+  if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
+    model <- mkinmod(parent = list(type = model))
+  }
+  initial_state = c(1, rep(0, length(model$diffs) - 1))
+  names(initial_state) <- names(model$diffs)
+  time_course <- mkinpredict(model, odeparms = parms, 
+                             odeini = initial_state,
+                             outtimes = times,
+                             solution_type = ifelse(length(model$spec) == 1,
+                                                    "analytical", "deSolve"))
+  invisible(time_course)
+}
diff --git a/pkg/man/PEC_sw_drift_ini.Rd b/pkg/man/PEC_sw_drift_ini.Rd
new file mode 100644
index 0000000..0bcbf97
--- /dev/null
+++ b/pkg/man/PEC_sw_drift_ini.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_sw_drift_ini.R
+\name{PEC_sw_drift_ini}
+\alias{PEC_sw_drift_ini}
+\title{Calculate initial predicted environmental concentrations in surface water due to drift}
+\usage{
+PEC_sw_drift_ini(rate, applications = 1, water_depth = 30,
+  drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20),
+  rate_units = "g/ha", PEC_units = "µg/L")
+}
+\arguments{
+\item{rate}{Application rate in units specified below}
+
+\item{applications}{Number of applications for selection of drift percentile}
+
+\item{water_depth}{Depth of the water body in cm}
+
+\item{drift_data}{Source of drift percentage data}
+
+\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"}
+
+\item{distances}{The distances in m for which to get PEC values}
+
+\item{rate_units}{Defaults to g/ha}
+
+\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported}
+}
+\value{
+The predicted concentration in surface water
+}
+\description{
+This is a basic, vectorised form of a simple calculation of a contaminant
+concentration in surface water based on complete, instantaneous mixing
+with input via spray drift.
+}
+\examples{
+PEC_sw_drift_ini(100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd
new file mode 100644
index 0000000..967b60f
--- /dev/null
+++ b/pkg/man/SFO_actual_twa.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/SFO_actual_twa.R
+\name{SFO_actual_twa}
+\alias{SFO_actual_twa}
+\title{Actual and maximum moving window time average concentrations for SFO kinetics}
+\source{
+FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1,
+  18 December 2014, p. 251
+}
+\usage{
+SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50,
+  100))
+}
+\arguments{
+\item{DT50}{The half-life.}
+
+\item{times}{The output times, and window sizes for time weighted average concentrations}
+}
+\description{
+Actual and maximum moving window time average concentrations for SFO kinetics
+}
+\examples{
+SFO_actual_twa(10)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd
new file mode 100644
index 0000000..b875434
--- /dev/null
+++ b/pkg/man/pfm_degradation.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/pfm_degradation.R
+\name{pfm_degradation}
+\alias{pfm_degradation}
+\title{Calculate a time course of relative concentrations based on an mkinmod model}
+\usage{
+pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
+  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
+  step_days))
+}
+\arguments{
+\item{model}{The degradation model to be used. Either a parent only model like
+'SFO' or 'FOMC', or an mkinmod object}
+
+\item{DT50}{The half-life. This is only used when simple exponential decline
+is calculated (SFO model).}
+
+\item{parms}{The parameters used for the degradation model}
+
+\item{years}{For how many years should the degradation be predicted?}
+
+\item{step_days}{What step size in days should the output have?}
+
+\item{times}{The output times}
+}
+\description{
+Calculate a time course of relative concentrations based on an mkinmod model
+}
+\examples{
+pfm_degradation("SFO", DT50 = 10)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/tests/testthat/test_SFO_actual_twa.R b/pkg/tests/testthat/test_SFO_actual_twa.R
new file mode 100644
index 0000000..b0a5537
--- /dev/null
+++ b/pkg/tests/testthat/test_SFO_actual_twa.R
@@ -0,0 +1,13 @@
+library(pfm)
+context("Actual and time weighted average concentrations for SFO kinetics")
+
+test_that("SFO_actual_twa calculates correctly", {
+  test_times <- c(0, 1, 7, 21, 42)
+  # This was calculated with the CRD spreadsheet for multiple applications
+  reference <- data.frame(
+    actual = c(10, 9.330, 6.156, 2.333, 0.544),
+    twa = c(NaN, 9.661, 7.923, 5.267, 3.248),
+    row.names = test_times)
+  result <- round(10 * SFO_actual_twa(10, times = test_times), 3)
+  expect_equal(result, reference)
+})