Merge pull request #31 from Burke-Lauenroth-Lab/newagg

New overall aggregation 'dailyNRCS_Maestas2016_ResilienceResistance' Former-commit-id: a5f7ee40e8fafea2a5595b2fd2f53e133c9d2aa1 [formerly 53be61d307013c70d59d412261b453d7a68830f1] Former-commit-id: 43d1ce1
DrylandEcology · Oct 4, 2016 · da85e09 · da85e09
2 parents 0a243c4 + 04cb829
commit da85e09
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Showing 3 changed files with 54 additions and 7 deletions.
diff --git a/2_SWSF_p1of5_Settings_v51.R b/2_SWSF_p1of5_Settings_v51.R
@@ -370,6 +370,7 @@ output_aggregates <- c(
 					#---Aggregation: Ecological dryness
 						"dailyNRCS_SoilMoistureTemperatureRegimes", 0, #Requires at least soil layers at 10, 20, 30, 50, 60, 90 cm
 						"dailyNRCS_Chambers2014_ResilienceResistance", 0, #Requires "dailyNRCS_SoilMoistureTemperatureRegimes"
+					  "dailyNRCS_Maestas2016_ResilienceResistance", 0,
 						"dailyWetDegreeDays", 1,
 						"dailyThermalDrynessStartEnd", 1,
 						"dailyThermalSWPConditionCount", 1,

diff --git a/R/2_SWSF_p2of5_CreateDB_Tables_v51.R b/R/2_SWSF_p2of5_CreateDB_Tables_v51.R
@@ -818,11 +818,25 @@ if(any(simulation_timescales=="daily") && aon$dailyNRCS_SoilMoistureTemperatureR
                     c("Anhydrous", "Aridic", "Udic", "Ustic", "Xeric")))))
     }
 	#35b
-		if(any(simulation_timescales=="daily") && aon$dailyNRCS_Chambers2014_ResilienceResistance && aon$dailyNRCS_SoilMoistureTemperatureRegimes){
-			cats <- c("Low", "ModeratelyLow", "Moderate", "ModeratelyHigh", "High")
-			temp <- c(temp, paste0("NRCS_Sagebrush", rep(c("Resilience", "Resistance"), each=length(cats)), "_", cats))
-			rm(cats)
-		}
+    if (any(simulation_timescales == "daily") &&
+        aon$dailyNRCS_Chambers2014_ResilienceResistance &&
+        aon$dailyNRCS_SoilMoistureTemperatureRegimes) {
+
+      cats <- c("Low", "ModeratelyLow", "Moderate", "ModeratelyHigh", "High")
+      temp <- c(temp, paste0("NRCS_Chambers2014_Sagebrush",
+                            rep(c("Resilience", "Resistance"), each = length(cats)),
+                            "_", cats))
+      rm(cats)
+    }
+
+    #35c
+    if (any(simulation_timescales == "daily") &&
+        aon$dailyNRCS_Maestas2016_ResilienceResistance &&
+        aon$dailyNRCS_SoilMoistureTemperatureRegimes) {
+
+      temp <- c(temp, paste0("NRCS_Maestas2016_SagebrushRR_", c("Low", "Moderate", "High")))
+    }
+
 	#35.2
 		if(any(simulation_timescales=="daily") & aon$dailyWetDegreeDays){
 			temp <- c(temp, paste("WetDegreeDays.SWPcrit", rep(fieldtag_SWPcrit_MPa, each=3), rep(c(".topLayers", ".bottomLayers", ".anyLayer"), times=length(SWPcrit_MPa)), "_Cdays_mean", sep=""))

diff --git a/R/2_SWSF_p4of5_Code_v51.R b/R/2_SWSF_p4of5_Code_v51.R
@@ -4176,10 +4176,42 @@ do_OneSite <- function(i_sim, i_labels, i_SWRunInformation, i_sw_input_soillayer
 					resMeans[nv:(nv+2*length(cats)-1)] <- c(resilience, resistance)
 					nv <- nv + 2*length(cats)
 
-					rm(cats, resilience, resistance, Tregime, Sregime)
+					rm(cats, resilience, resistance)
 
 				}
-				rm(regimes_done)
+
+        #35c
+        if(any(simulation_timescales=="daily") && aon$dailyNRCS_Maestas2016_ResilienceResistance && aon$dailyNRCS_SoilMoistureTemperatureRegimes){	#Requires "dailyNRCS_SoilMoistureTemperatureRegimes"
+          #Based on Maestas, J.D., Campbell, S.B., Chambers, J.C., Pellant, M. & Miller, R.F. (2016). Tapping Soil Survey Information for Rapid Assessment of Sagebrush Ecosystem Resilience and Resistance. Rangelands, 38, 120-128.
+          if (print.debug)
+            print("Aggregation of dailyNRCS_Maestas2016_ResilienceResistance")
+
+          RR <- c(Low = 0, Moderate = 0, High = 0)
+
+          if (regimes_done) {
+            #---Table 1 in Maestas et al. 2016
+            Table1 <- matrix(c(
+                "Cryic", "Xeric", "High",
+                "Frigid", "Xeric", "High",
+                "Cryic", "Aridic", "Moderate",
+                "Frigid", "Aridic", "Moderate",
+                "Mesic", "Xeric", "Moderate",
+                "Mesic", "Aridic", "Low"),
+              ncol = 3, byrow = TRUE)
+
+            temp <- Table1[as.logical(Tregime[Table1[, 1]]) & as.logical(Sregime[Table1[, 2]]), 3]
+            RR[temp] <- 1
+
+            rm(Table1)
+          }
+
+          nv_new <- nv + length(cats)
+          resMeans[nv:(nv_new - 1)] <- RR
+          nv <- nv_new
+
+          rm(RR)
+        }
+        rm(regimes_done, Tregime, Sregime)
 
 			#35.2
 				if(any(simulation_timescales=="daily") & aon$dailyWetDegreeDays){	#Wet degree days on daily temp and swp