Merge pull request DrylandEcology#6 from aestears/main

changes AES has made to the grid stdf so far
aestears · Jun 12, 2024 · c4c6b84 · c4c6b84
2 parents 79769ba + 4891211
commit c4c6b84
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Showing 17 changed files with 3,252 additions and 3,204 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -13,4 +13,5 @@ HPC_Files/Outs/
 projects/06_TestOutputs/*.csv
 projects/07_TestOutputForFRESC/*.zip
 projects/07_TestOutputForFRESC/full_netCDFs.zip
-./projects/07_TestOutputForFRESC/trimmed_netCDFs.zip
+./projects/07_TestOutputForFRESC/trimmed_netCDFs.zip
+Main/Data/soilsDB/
diff --git a/functions/formatEcologicalIndicatorOutput.R b/functions/formatEcologicalIndicatorOutput.R
@@ -75,11 +75,11 @@ formatOConnor2020 <- function(Hist_OConnor2020, Future_OConnor2020) {
   All <- rbind(Hist_OConnor2020, Future_OConnor2020)
 
   # get stats
-  Outs <- setDT(All)[, .(sTemp_mean = mean(Lyr_1),
-                         sTemp_CI95 = std(Lyr_1 * 1.96),
+  Outs <- setDT(All)[, .(sTemp_mean = mean(Lyr_1_avg_C),
+                         sTemp_CI95 = std(Lyr_1_avg_C * 1.96),
                          SWP_mean = mean(SWP),
                          SWP_CI95 = std(SWP) * 1.96),
                      .(Date, TP)]
 
   return(Outs)
-}
+}
diff --git a/functions/getEcologicalIndicatorsInputs.R b/functions/getEcologicalIndicatorsInputs.R
@@ -40,8 +40,8 @@ getOConnor2020Vars <- function(sTempDF, VWCDF, SoilsDF, TimePeriod,
                                currDate = currDate) {
 
   # Soil texture values
-  sand <- as.numeric(SoilsDF[1, 'sand_frac'])/100
-  clay <- as.numeric(SoilsDF[1, 'clay_frac'])/100
+  sand <- as.numeric(SoilsDF[1, 'sand_frac'])
+  clay <- as.numeric(SoilsDF[1, 'clay_frac'])
 
   if(TimePeriod == 'Future') {
 
@@ -71,7 +71,7 @@ getOConnor2020Vars <- function(sTempDF, VWCDF, SoilsDF, TimePeriod,
   # soil temp: 0 - 5cm, mean and std. error * 1.96
   # SWP: 0 -5cm, mean and SE * 1.96
   # all days
-  sTemp_top <- sTempDF[, c('Year', 'Day', 'Lyr_1', 'TP')]
+  sTemp_top <- sTempDF[, c('Year', 'Day', 'Lyr_1_avg_C', 'TP')] # do we want the average temp? (is basically the same)
   sTemp_top <- makeDateMonthDat(sTemp_top, 'Day')
   sTemp_top <- sTemp_top[sTemp_top$Date %in% c(paste0('03-0',1:9),paste0('03-',10:31)) ,]
 
@@ -81,13 +81,14 @@ getOConnor2020Vars <- function(sTempDF, VWCDF, SoilsDF, TimePeriod,
   VWC_top <- makeDateMonthDat(VWC_top, 'Day')
   VWC_top <- VWC_top[VWC_top$Date %in% c(paste0('03-0',1:9),paste0('03-',10:31)) ,]
 
-  VWC_top$SWP <- rSOILWAT2::VWCtoSWP(VWC_top$value, sand, clay)
+  VWC_top$SWP <- rSOILWAT2::swrc_vwc_to_swp(vwcBulk = VWC_top$value, sand = sand, clay = clay)
   VWC_top$SWP <- ifelse(VWC_top$SWP < -8, -8, VWC_top$SWP)
 
   # statistics taken in format step
-  vars <- merge(sTemp_top[,c('Date', 'Year', 'TP','Lyr_1')],
+  vars <- merge(sTemp_top[,c('Date', 'Year', 'TP','Lyr_1_avg_C')],
                 VWC_top[,c('Date', 'Year', 'TP', 'SWP')],  by = c('Year','Date', 'TP'))
 
   return(vars)
 
-}
+}
+
diff --git a/functions/getOutputs.R b/functions/getOutputs.R
@@ -31,8 +31,8 @@ getOutputs <- function(sw_out, sw_in, SoilsDF, calc_EcoVars = TRUE,
     Shriver2018Vars <- getShriver2018Vars(Data, VWC1)
 
     #OConnor Vars
-    #Oconnor2020Vars <- getOConnor2020Vars(sTemp, VWC1, SoilsDF, TimePeriod,
-    #                                     currYear, currDate)
+    Oconnor2020Vars <- getOConnor2020Vars(sTemp, VWC1, SoilsDF, TimePeriod,
+                                         currYear, currDate)
 
     GISSM_1 <- suppressWarnings(rSW2funs::calc_GISSM(
       x = sw_out,
@@ -77,8 +77,8 @@ getOutputs <- function(sw_out, sw_in, SoilsDF, calc_EcoVars = TRUE,
   if(!calc_EcoVars) return(list(Data))
   if(calc_EcoVars) return(list(Data, 
                                Shriver2018Vars,
-                               data.table(GISSM_1[[1]])))
-                               #Oconnor2020Vars))
+                               data.table(GISSM_1[[1]]),#))
+                               Oconnor2020Vars))
 
 }