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()

2 files changed, 82 insertions, 0 deletions

diff --git a/inst/dataset_generation/D24_2014.R b/inst/dataset_generation/D24_2014.R
new file mode 100644
index 00000000..bea74da5
--- /dev/null
+++ b/inst/dataset_generation/D24_2014.R
@@ -0,0 +1,71 @@
+# From the Addendum to the RAR 2014, see the help file for D24_2014
+# Soil characterisation from EFSA conclusion 2014
+D24_2014 <- mkindsg$new(
+  title = "Aerobic soil degradation data on 2,4-D from the EU assessment in 2014",
+  ds = list(
+    mkinds$new("Mississippi",
+      data.frame(
+        name = "D24",
+        time = c(0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365),
+        value = c(96.8, 81.0, 81.7, 88.2, 66.3, 72.9, 62.6, 54.6, 35.2, 18.0,
+          11.3, 9.9, 6.3))
+    ),
+    mkinds$new("Fayette",
+      mkin_wide_to_long(
+        data.frame(
+          t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2),
+          D24 = c(96.9, 96.6, 93.2, 93.2, 90.5, 91.5, 86.3, 87.1, 79.0, 80.8,
+            74.0, 65.6, 35.0, 36.7, 6.6, 4.5, 1.6, 1.7),
+          DCP = c(NA, NA, 1.4, 1.6, 2.5, 2.4, 2.9, 3.1, 4.4, 4.2, 5.8, 5.4,
+            8.2, 8.7, 5.8, 3.8, 1.8, 2.0),
+          DCA = c(rep(NA, 10), 3.2, 3.5, 9.5, 9.1, 15.0, 13.0, 11.8, 11.7))
+      )
+    ),
+    mkinds$new("RefSol 03-G",
+      mkin_wide_to_long(
+        data.frame(
+          t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2),
+          D24 = c(92.9, 93.1, 87.4, 87.9, 78.1, 78.8, 57.1, 56.1, 25.0, 32.3,
+            14.7, NA, 3.1, 3.1, 2.7, 2.1, 2.0, 2.2),
+          DCP = c(NA, NA, 2.8, 2.5, 5.5, 5.4, 8.5, 8.6, 6.7, 5.3, 5.7, NA,
+            3.2, 2.7, 2.3, 1.7, 1.3, 1.7),
+          DCA = c(rep(NA, 6), 3.3, 3.7, 8.0, 7.0, 10.6, NA, 7.7, 7.9, 5.2,
+            6.7, 4.6, 4.2))
+      )
+    ),
+    mkinds$new("Site E1",
+      mkin_wide_to_long(
+        data.frame(
+          t = rep(c(0, 0.1, 0.3, 1, 3, 7, 10, 17, 26), each = 2),
+          D24 = c(97.5, 97.9, 97.9, 98.3, 92.4, 91.9, 65.8, 69.5, 37.5,
+            40, 18.8, 14.4, 3.3, 5.7, 2.6, 2.3, 2.4, 2),
+          DCP = c(rep(NA, 4), 1.8, 2.3, 4.4, 3.6, 4.8, 4.3, 3.3, 3.7,
+            1.7, 2.3, NA, 0.8, 0.8, 0.8),
+          DCA = c(rep(NA, 6), 3.9, 2.9, 6.3, 5.4, 5.7, 5.5, 4.5, 4.2,
+            3.0, 2.5, 1.5, 1.7))
+      )
+    ),
+    mkinds$new("Site I2",
+      mkin_wide_to_long(
+        data.frame(
+          t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2),
+          D24 = c(94.1, 91.6, 90.1, 89.2, 86.3, 86.5, 76.7, 74.7,
+            33.1, NA, 8.8, 6.7, 3.1, 3.2, 1.6, 1.7, 1.5, 1.9),
+          DCP = c(NA, NA, 0.9, 1.2, 1.7, 1.3, 2.5, 5.1, 2.5, NA,
+            1.9, 1.7, 0.5, 0.9, 0.9, 1.2, 0.7, NA),
+          DCA = c(rep(NA, 8), 4.5, NA, 6.6, 5.7, 5.1, 4.3, 2.3, 2.2,
+            2.1, 2.1))
+      )
+    )
+  ),
+  meta = data.frame(
+    study = c("Cohen 1991", rep("Liu and Adelfinskaya 2011", 4)),
+    usda_soil_type = c("Silt loam", # p. 683
+      "Clay loam", "Clay loam", "Sandy loam", "Sandy loam"), # EFSA 204 p. 41/42
+    moisture_ref_type = c(NA, rep("% MWHC", 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)
diff --git a/inst/dataset_generation/focus_soil_moisture.R b/inst/dataset_generation/focus_soil_moisture.R
new file mode 100644
index 00000000..bfabc29a
--- /dev/null
+++ b/inst/dataset_generation/focus_soil_moisture.R
@@ -0,0 +1,11 @@
+# FOCUS Generic GW 2014, p. 36
+focus_soil_moisture <- as.matrix(
+  data.frame(
+    usda_soil_type = c("Sand", "Loamy sand", "Sandy loam", "Sandy clay loam",
+      "Clay loam", "Loam", "Silt loam", "Silty clay loam", "Silt",
+      "Sandy clay", "Silty clay", "Clay"),
+    pF1 = c(24, 24, 27, 28, 32, 31, 32, 34, 31, 41, 44, 53),
+    pF2 = c(12, 14, 19, 22, 28, 25, 26, 30, 27, 35, 40, 48),
+    pF2.5 = c(7, 9, 15, 18, 25, 21, 21, 27, 21, 31, 36, 43),
+    row.names = "usda_soil_type"))
+#save(focus_soil_moisture, file = "../../data/focus_soil_moisture.rda", version = 2)