From 7b807680b66269ff911df137f56e26775d84e283 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 12 Nov 2020 11:04:45 +0100
Subject: mkindsg class to hold groups of datasets

- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU
  assessment as mkindsg object with metadata
- f_time_norm_focus() to do time-step normalisation using the FOCUS
  method
- focus_soil_moisture data with default moisture contents at pF1,
  pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance
- Dataset generation scripts in inst/dataset_generation
- Depend on R >= 2.15.1 in order to facilitate the use of
  utils::globalVariables()
---
 R/f_time_norm_focus.R | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 R/f_time_norm_focus.R

(limited to 'R/f_time_norm_focus.R')

diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R
new file mode 100644
index 00000000..be5cf583
--- /dev/null
+++ b/R/f_time_norm_focus.R
@@ -0,0 +1,77 @@
+utils::globalVariables("D24_2014")
+
+#' Normalisation factors for aerobic soil degradation according to FOCUS guidance
+#'
+#' Time step normalisation factors for aerobic soil degradation as described
+#' in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).
+#'
+#' @param object An object containing information used for the calculations
+#' @param temperature Numeric vector of temperatures in °C
+#' @param moisture Numeric vector of moisture contents in \\% w/w
+#' @param field_moisture Numeric vector of moisture contents at field capacity
+#'   (pF2) in \\% w/w
+#' @param Q10 The Q10 value used for temperature normalisation
+#' @param walker The Walker exponent used for moisture normalisation
+#' @param f_na The factor to use for NA values. If set to NA, only factors
+#'  for complete cases will be returned.
+#' @param \dots Currently not used
+#' @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}
+#' FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+#'   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+#'   EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+#'   Version 1.1, 18 December 2014
+#'   \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+#' @seealso [focus_soil_moisture]
+#' @examples
+#' f_time_norm_focus(25, 20, 25) # 1.37, compare p. 184
+#'
+#' D24_2014$meta
+#' # No moisture normalisation in the first dataset, so we use f_na = 1 to get
+#' # Temperature only normalisation as in the EU evaluation
+#' f_time_norm_focus(D24_2014, f_na = 1)
+#' # Moisture normalisation for the other four soils is one, as soil moisture
+#' # is higher than the approximate field capacity derived from the USDA soil
+#' # type
+#' @export
+f_time_norm_focus <- function(object, ...) {
+  UseMethod("f_time_norm_focus")
+}
+
+#' @rdname f_time_norm_focus
+#' @export
+f_time_norm_focus.numeric <- function(object, 
+  moisture = NA, field_moisture = NA, 
+  temperature = object, 
+  Q10 = 2.58, walker = 0.7, f_na = NA, ...)
+{
+  f_temp <- ifelse(is.na(temperature),
+    f_na,
+    ifelse(temperature <= 0,
+      0,
+      Q10^((temperature - 20)/10)))
+  f_moist <- ifelse(is.na(moisture),
+    f_na,
+    ifelse(moisture >= field_moisture,
+      1,
+      (moisture / field_moisture)^walker))
+  f_time_norm <- f_temp * f_moist
+  f_time_norm
+}
+
+#' @rdname f_time_norm_focus
+#' @export
+f_time_norm_focus.mkindsg <- function(object, Q10 = 2.58, walker = 0.7, f_na = NA, ...) {
+  meta <- object$meta
+  field_moisture <- focus_soil_moisture[meta$usda_soil_type, "pF2"]
+  study_moisture <- meta$rel_moisture * meta$moisture_ref
+  object$f_time_norm <- f_time_norm_focus(meta$temperature,
+    moisture = study_moisture, field_moisture = field_moisture,
+    Q10 = Q10, walker = walker, f_na = f_na)
+  cat("$time_norm was set to\n")
+  print(object$f_time_norm)
+}
-- 
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