Fixes for f_time_norm_focus, still very fragile...

4 files changed, 49 insertions, 18 deletions

diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R
index be5cf583..66df527e 100644
--- a/R/f_time_norm_focus.R
+++ b/R/f_time_norm_focus.R
@@ -10,6 +10,8 @@ utils::globalVariables("D24_2014")
 #' @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 study_moisture_ref_source Source for the reference value
+#'   used to calculate the study moisture
 #' @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
@@ -28,15 +30,12 @@ utils::globalVariables("D24_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
+#' f_time_norm_focus(25, 20, 25) # 1.37, compare FOCUS 2014 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
+#' # temperature only normalisation as in the EU evaluation
+#' f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1)
 #' @export
 f_time_norm_focus <- function(object, ...) {
   UseMethod("f_time_norm_focus")
@@ -44,9 +43,9 @@ f_time_norm_focus <- function(object, ...) {
 
 #' @rdname f_time_norm_focus
 #' @export
-f_time_norm_focus.numeric <- function(object, 
-  moisture = NA, field_moisture = NA, 
-  temperature = object, 
+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),
@@ -65,13 +64,40 @@ f_time_norm_focus.numeric <- function(object,
 
 #' @rdname f_time_norm_focus
 #' @export
-f_time_norm_focus.mkindsg <- function(object, Q10 = 2.58, walker = 0.7, f_na = NA, ...) {
+f_time_norm_focus.mkindsg <- function(object,
+  study_moisture_ref_source = c("meta", "focus"),
+  Q10 = 2.58, walker = 0.7, f_na = NA, ...) {
+
+  study_moisture_ref_source <- match.arg(study_moisture_ref_source)
   meta <- object$meta
-  field_moisture <- focus_soil_moisture[meta$usda_soil_type, "pF2"]
-  study_moisture <- meta$rel_moisture * meta$moisture_ref
+
+  if (is.null(meta$field_moisture)) {
+    field_moisture <- focus_soil_moisture[meta$usda_soil_type, "pF2"]
+  } else {
+    field_moisture <- ifelse(is.na(meta$field_moisture),
+      focus_soil_moisture[meta$usda_soil_type, "pF2"],
+      meta$field_moisture)
+  }
+
+  if (study_moisture_ref_source == "meta") {
+    study_moisture_ref <- meta$study_moisture_ref
+  } else {
+    study_moisture_ref <-
+      focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]
+  }
+
+  if ("study_moisture" %in% names(meta)) {
+    study_moisture <- ifelse(is.na(meta$study_moisture),
+      meta$rel_moisture * study_moisture_ref,
+      meta$study_moisture)
+  } else {
+    study_moisture <- meta$rel_moisture * study_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)
+  return(object$f_time_norm)
 }
diff --git a/R/focus_soil_moisture.R b/R/focus_soil_moisture.R
index 7b22fbcc..ef67aec2 100644
--- a/R/focus_soil_moisture.R
+++ b/R/focus_soil_moisture.R
@@ -2,6 +2,9 @@ utils::globalVariables("focus_soil_moisture")
 
 #' FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
 #'
+#' The value were transcribed from p. 36. The table assumes field capacity
+#' corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.
+#'
 #' @format A matrix with upper case USDA soil classes as row names, and water tension
 #'   ('pF1', 'pF2', 'pF 2.5') as column names
 #' @source Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment
diff --git a/data/D24_2014.rda b/data/D24_2014.rda
index 5777ca89..ef796e4d 100644
--- a/data/D24_2014.rda
+++ b/data/D24_2014.rda
diff --git a/inst/dataset_generation/D24_2014.R b/inst/dataset_generation/D24_2014.R
index 47f9cfab..435be4a6 100644
--- a/inst/dataset_generation/D24_2014.R
+++ b/inst/dataset_generation/D24_2014.R
@@ -1,5 +1,8 @@
 # From the Addendum to the RAR 2014, see the help file for D24_2014
-# Soil characterisation from EFSA conclusion 2014
+# Soil characterisation in the EFSA conclusion 2014 is completely different
+# and does not correspond to the USDA soil types that can be derived
+# from the texture data on p. 687
+library(mkin)
 D24_2014 <- mkindsg$new(
   title = "Aerobic soil degradation data on 2,4-D from the EU assessment in 2014",
   ds = list(
@@ -60,12 +63,11 @@ D24_2014 <- mkindsg$new(
   ),
   meta = data.frame(
     study = c("Cohen 1991", rep("Liu and Adelfinskaya 2011", 4)),
-    usda_soil_type = c("Silt loam", # p. 683, EFSA conclusion p. 41/42
-      "Clay loam", "Clay loam", "Sandy loam", "Sandy loam"),
-    moisture_ref_type = c(NA, rep("% MWHC", 4)), # p. 687
+    usda_soil_type = c("Silt loam", # p. 683, 687
+      "Silt loam", "Loam", "Loam", "Loamy sand"),
+    study_moisture_ref_type = c(NA, rep("pF1", 4)), # p. 687
     rel_moisture = c(NA, 0.5, 0.5, 0.5, 0.5), # p. 687
-    moisture_ref = c(NA, 65.7, 59.9, 75.3, 48.5), # p. 687
     temperature = c(25, 20, 20, 20, 20)
   )
 )
-#save(D24_2014, file = "../../data/D24_2014.rda", version = 2)
+save(D24_2014, file = "../../data/D24_2014.rda", version = 2)