Merge commit 'stash@{2}' into generalized_agg_funs

Working on implementing 'agg_fun' aggregations (part 7) Former-commit-id: a1f6a24
DrylandEcology · Oct 11, 2016 · 21cc475 · 21cc475
2 parents 47fe79f + 5f94d34
commit 21cc475
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Showing 4 changed files with 254 additions and 79 deletions.
diff --git a/2_SWSF_p1of5_Settings_v51.R b/2_SWSF_p1of5_Settings_v51.R
@@ -459,12 +459,12 @@ daily_lyr_agg <- list(
 
 #regeneration: germination and establishment
 opts_regen_bySWPSnow <- list(
-  season.start = "LastSnow" # either doy or "LastSnow"
-  season.end = "FirstSnow" # either doy or "FirstSnow"
-  germination.duration = 7 # in days
-  germination.swp.surface = -0.2 # in MPa, duration must have at least x MPa
-  establishment.duration = 14 # in days
-  establishment.swp.surface = -0.4 # in MPa, duration must have at least x MPa
+  season.start = "LastSnow", # either doy or "LastSnow"
+  season.end = "FirstSnow", # either doy or "FirstSnow"
+  germination.duration = 7, # in days
+  germination.swp.surface = -0.2, # in MPa, duration must have at least x MPa
+  establishment.duration = 14, # in days
+  establishment.swp.surface = -0.4, # in MPa, duration must have at least x MPa
   establishment.delay = 1 # start of establishment needs to occur latest x days after end of germination
 )
 
@@ -478,6 +478,10 @@ growing.season.threshold.tempC <- 10 # based on Trewartha's D temperateness defi
 growing.season.threshold.tempC <- 4 # based on standard input of mean monthly biomass values for vegetation composition
 
 
+# dry soil periods: minimum duration to quality for aggregations 'dailySuitablePeriodsDrySpells' and 'dailySWPdrynessANDwetness'
+duration_min_drysoils_days <- 10	# used, e.g., by functions 'startDoyOfDuration' and 'endDoyOfDuration'
+
+
 #------SoilWat files
 sw <- "sw_v31"
 sw.inputs <- "Input"	#must be string of length > 0; i.e. not compatible with SoilWat versions < 21

diff --git a/R/2_SWSF_p2of5_CreateDB_Tables_v51.R b/R/2_SWSF_p2of5_CreateDB_Tables_v51.R
@@ -586,6 +586,7 @@ if (length(Tables) == 0 || cleanDB) {
 		fieldtag_Tmin_crit_C <- paste0(ifelse(Tmin_crit_C < 0, "Neg", ifelse(Tmin_crit_C > 0, "Pos", "")), abs(Tmin_crit_C), "C")
 		fieldtag_Tmax_crit_C <- paste0(ifelse(Tmax_crit_C < 0, "Neg", ifelse(Tmax_crit_C > 0, "Pos", "")), abs(Tmax_crit_C), "C")
 		fieldtag_Tmean_crit_C <- paste0(ifelse(Tmean_crit_C < 0, "Neg", ifelse(Tmean_crit_C > 0, "Pos", "")), abs(Tmean_crit_C), "C")
+    fieldtag_drysoils <- paste0("AtLeast", duration_min_drysoils_days, "Days")
 
 	#0.
 		if (aon$input_SoilProfile) {
@@ -960,19 +961,40 @@ if (length(Tables) == 0 || cleanDB) {
                       "_Count_days"))
 		}
 
-#TODO(drs): progress state
 	#36
 		if (aon$monthlySWPdryness) {
-			temp <- c(temp, paste("DrySoilPeriods.SWPcrit", rep(fieldtag_SWPcrit_MPa, times=2), ".NSadj.", rep(c("topLayers", "bottomLayers"), each=length(SWPcrit_MPa)), ".Duration.Total_months_mean", sep=""),
-					paste("DrySoilPeriods.SWPcrit", rep(fieldtag_SWPcrit_MPa, times=2), ".NSadj.", rep(c("topLayers", "bottomLayers"), each=length(SWPcrit_MPa)), ".Start_month_mean", sep=""))
+			temp <- c(temp, paste0("DrySoilPeriods.SWPcrit",
+                            rep(fieldtag_SWPcrit_MPa, times = 2), ".NSadj.",
+                            rep(c("topLayers", "bottomLayers"), each = length(SWPcrit_MPa)),
+                            ".Duration.Total_months"),
+                      paste0("DrySoilPeriods.SWPcrit",
+                            rep(fieldtag_SWPcrit_MPa, times = 2), ".NSadj.",
+                            rep(c("topLayers", "bottomLayers"), each = length(SWPcrit_MPa)),
+                            ".Start_month"))
 		}
 
 	#37
 		if (aon$dailySWPdrynessANDwetness) {
-			temp <- c(temp, paste(rep(c("WetSoilPeriods", "DrySoilPeriods"), each=8), ".SWPcrit", rep(fieldtag_SWPcrit_MPa, each=16), ".NSadj.", c(rep(c("topLayers", "bottomLayers"), times=4), rep(rep(c("topLayers", "bottomLayers"), each=2), times=2)),
-							rep(c(".AnyLayerWet.", ".AllLayersWet.", ".AllLayersDry.", ""), each=4), c(rep(rep(c("Duration.Total_days", "Duration.LongestContinuous_days"), each=2), times=2), rep(c("Duration.Total_days", "Duration.LongestContinuous_days"), times=2), rep(c(".PeriodsForAtLeast10Days.Start_doy", ".PeriodsForAtLeast10Days.End_doy"), times=2)), "_mean", sep=""))
+			temp <- c(temp, paste0(rep(c("WetSoilPeriods", "DrySoilPeriods"), each = 8),
+                            ".SWPcrit",
+                            rep(fieldtag_SWPcrit_MPa, each = 16),
+                            ".NSadj.",
+                            c(rep(c("topLayers", "bottomLayers"), times = 4),
+                              rep(rep(c("topLayers", "bottomLayers"), each = 2), times = 2)),
+                            rep(c(".AnyLayerWet", ".AllLayersWet", ".AllLayersDry", ""),
+                                each = 4),
+                            ".",
+                            c(rep(rep(c("Duration.Total_days",
+                                        "Duration.LongestContinuous_days"), each = 2),
+                                  times = 2),
+                              rep(c("Duration.Total_days",
+                                    "Duration.LongestContinuous_days"), times = 2),
+                              paste0("PeriodsFor", fieldtag_drysoils, ".",
+                                rep(c("Start_doy", "End_doy"), times = 2)))
+                            ))
 		}
 
+#TODO(drs): progress state
 	#38
 		if (aon$dailySuitablePeriodsDuration) {
 			quantiles <- c(0.05, 0.5, 0.95)
@@ -985,7 +1007,16 @@ if (length(Tables) == 0 || cleanDB) {
 		}
 	#40
 		if (aon$dailySuitablePeriodsDrySpells) {
-			temp <- c(temp, paste("ThermalSnowfreeDryPeriods.SWPcrit", rep(paste(rep(fieldtag_SWPcrit_MPa, each=2), rep(c(".topLayers", ".bottomLayers"), times=length(SWPcrit_MPa)), sep=""), each=4), c("_DrySpellsAllLayers_meanDuration_days_mean", "_DrySpellsAllLayers_maxDuration_days_mean", "_DrySpellsAllLayers_Total_days_mean", "_DrySpellsAtLeast10DaysAllLayers_Start_doy_mean"), sep=""))
+			temp <- c(temp, paste0("ThermalSnowfreeDryPeriods.SWPcrit",
+			                      rep(paste0(rep(fieldtag_SWPcrit_MPa, each = 2),
+			                                rep(c(".topLayers", ".bottomLayers"),
+			                                    times=length(SWPcrit_MPa))),
+			                          each=4),
+			                      "_DrySpells",
+			                      c(rep("", 3), fieldtag_drysoils),
+			                      "AllLayers_",
+			                      c("meanDuration_days", "maxDuration_days", "Total_days",
+			                        "Start_doy")))
 		}
 	#41
 		if (aon$dailySWPdrynessDurationDistribution) {
@@ -1169,7 +1200,7 @@ if (length(Tables) == 0 || cleanDB) {
 
 	#62
 		if (aon$dailyRegeneration_bySWPSnow) {
-			temp <- c(temp, "Regeneration.Potential.SuitableYears.NSadj_fraction_mean")
+			temp <- c(temp, "Regeneration.Potential.SuitableYears.NSadj_fraction")
 		}
 
 	#63