Modifying File Paths and Annotating

Model/MRM0D/RunModel_BATS_0D.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+
+#max_epsilon is the maximum exoenzyme production rate
+
+#qfrac is the fraction of the surface area of the spherical particle covered by a single layer of bacteria, values greater than 1 mean that there is a second layer of bacteria
+
+for max_epsilon in 0.0000 0.0005 0.0010 0.0015 0.0020 0.0025 0.0030 0.0035 0.0040 0.0045 0.0050 0.0055 0.0060 0.0065 0.0070 0.0075 0.0080 0.0085 0.0090 0.0095 0.0100 0.0105 0.0110 0.0115 0.0120 0.0125 0.0130 0.0135 0.0140 0.0145 0.0150 0.0155 0.0160 0.0165 0.0170 0.0175 0.0180 0.0185 0.0190 0.0195 0.0200 0.0205 0.0210 0.0215 0.0220 0.0225 0.0230 0.0235 0.0240 0.0245 0.0250 0.0255 0.0260 0.0265 0.0270 0.0275 0.0280 0.0285 0.0290 0.0295 0.0300 0.0305 0.0310 0.0315 0.0320 0.0325 0.0330 0.0335 0.0340 0.0345 0.0350 0.0355 0.0360 0.0365 0.0370 0.0375 0.0380 0.0385 0.0390 0.0395 0.0400 0.0405 0.0410 0.0415 0.0420 0.0425 0.0430 0.0435 0.0440 0.0445 0.0450 0.0455 0.0460 0.0465 0.0470 0.0475 0.0480 0.0485 0.0490 0.0495 0.0500
+do
+for qfrac in 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10
+do
+	rm MassTransferRates.out
+	rm StateVariables.out
+	rm BacteriaRates.out
+	rm grow2.input
+	echo "&control" > grow2.input
+	echo "qfrac =" ${qfrac} >> grow2.input
+	echo "max_epsilon =" ${max_epsilon} >> grow2.input
+	echo "/" >> grow2.input
+	echo " " >> grow2.input
+
+./MRM0D1 < grow2.input
+cp StateVariables.out ../../Output/MRM0D/StateVariables/StateVariables_maxe${max_epsilon}_qfrac${qfrac}.out
+cp BacteriaRates.out ../../Output/MRM0D/BacteriaRates/BacteriaRates_maxe${max_epsilon}_qfrac${qfrac}.out
+cp MassTransferRates.out ../../Output/MRM0D/MassTransferRates/MassTransferRates_maxe${max_epsilon}_qfrac${qfrac}.out
+done
+done

Model/MRM0D/grow2.input

@@ -0,0 +1,5 @@
+&control
+qfrac = 0.47
+max_epsilon = 0.0075
+/
+

Model/RunModel_BATS_CFlux1D.sh → Model/MRM1D/RunModel_BATS_1D.sh

@@ -27,9 +27,9 @@ do
 	echo "/" >> sizesink.input
 	echo " " >> sizesink.input
 
-./MRM1 < sizesink.input
-cp StateVariables.out ../Output/StateVariables/StateVariables_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
-cp BacteriaRates.out ../Output/BacteriaRates/BacteriaRates_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
-cp MassTransferRates.out ../Output/MassTransferRates/MassTransferRates_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
+./MRM1D1 < sizesink.input
+cp StateVariables.out ../../Output/MRM1D/StateVariables/StateVariables_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
+cp BacteriaRates.out ../../Output/MRM1D/BacteriaRates/BacteriaRates_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
+cp MassTransferRates.out ../../Output/MRM1D/MassTransferRates/MassTransferRates_Sink${w}_Size${r_top}_Qfrac${qfrac}.out
 done
 done

Output/MRM1D/MassTransferRates/.gitignore

@@ -0,0 +1 @@
+*.out

Output/MRM1D/StateVariables/.gitignore

@@ -0,0 +1 @@
+*.out

RCode/DataToInput/BATS_CTDTables.R

@@ -1,17 +1,25 @@
-##Data Input
-source("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/RCode/sigmat.fun")
-source("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/RCode/thetap.fun")
-source("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/RCode/alr.fun")
+#Change working directory to MicrobeReminModel_v1.0 using the setwd() command or using the Misc menu.  
+getwd() #shows the current working directory for the R gui.  
 
-DataFolder<-paste("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/CTD/", sep="")
-DataFiles<-list.files(DataFolder)
+#---------------------
+# Source R Functions
+#---------------------
+source("RCode/R_functions/sigmat.fun")
+source("RCode/R_functions/thetap.fun")
+source("RCode/R_functions/alr.fun")
 
-#quartz()
-#plot(CTD$Temp, CTD$Depth*-1, type="l")
+#------------------------------
+# Read in List of Data Files
+#------------------------------
 
-depths<-seq(150, 4000, 10)
+DataFolder<-paste("Data/BATS/CTD/", sep="")
+DataFiles<-list.files(DataFolder)
 
-#depths<-seq(10, 50, 10)
+#-----------------
+# Create Tables
+#-----------------
+
+depths<-seq(150, 4000, 10) # Final data in 10 m intervals
 
 TempTable<-as.data.frame(matrix(NA, length(depths), 1))
 colnames(TempTable)<-c("Depth")
@@ -23,6 +31,10 @@ RhoTable<-as.data.frame(matrix(NA, length(depths), 1))
 colnames(RhoTable)<-c("Depth")
 RhoTable$Depth<-depths
 
+#----------------------------
+# Read and Process CTD Data
+#----------------------------
+
 for(k in 1:length(DataFiles)){
 
 FileName<-paste(DataFolder, DataFiles[k], sep="")
@@ -33,11 +45,12 @@ colnames(CTD)<-c("ID", "Date", "Lat", "Lon", "Pres", "Depth", "Temp", "Sal", "DO
 
 CTD<-CTD[c("ID", "Date", "Pres","Depth","Temp","Sal")]
 
+#Replace Bad Values with NA
 CTD$Sal<-ifelse(CTD$Sal<0, NA, CTD$Sal)
 CTD$Sal<-ifelse(CTD$Sal>38, NA, CTD$Sal)
 CTD$Temp<-ifelse(CTD$Temp<0, NA, CTD$Temp)
 
-
+#Time Process
 CTD$Year<-floor(CTD$Date)
 CTD$Yfrac<-CTD$Date-CTD$Year
 CTD$Sfrac<-unclass(ISOdate(CTD$Year+1,1,1,0,0,0)) - unclass(ISOdate(CTD$Year,1,1,0,0,0))
@@ -46,53 +59,45 @@ CTD$Date<-substr(CTD$Date2,1,10)
 
 CTD$Cast<-substr(CTD$ID, 6, 7)
 
+#Average CTD casts done on the same day
 CTDagg<-aggregate(CTD[c("Pres", "Temp", "Sal")], list(CTD[,c("Year")], CTD[,c("Date")], CTD[,c("Depth")]), mean, na.rm=TRUE)
-
 colnames(CTDagg)<-c("Year","Date","Depth","Pres", "Temp", "Sal")
-
-
 CTDagg$Depth<-round(CTDagg$Depth, digits=0)
 
+#Interpolate CTD data
 CTDinterp<-as.data.frame(matrix(NA, max(CTDagg$Depth), 2))
 colnames(CTDinterp)<-c("Depth","Blank")
 CTDinterp$Depth<-as.numeric(row.names(CTDinterp))
 CTDinterp<-subset(CTDinterp, CTDinterp$Depth>=min(CTDagg$Depth, na.rm=TRUE))
-
 CTDinterp2<-merge(CTDinterp, CTDagg, all=TRUE)
 CTDinterp2<-CTDinterp2[,-2]
-
-
 p1<-approx(CTDinterp2$Depth, CTDinterp2$Pres, CTDinterp2$Depth)
 CTDinterp2$Pres<-p1$y
-
 t1<-approx(CTDinterp2$Depth, CTDinterp2$Temp, CTDinterp2$Depth)
 CTDinterp2$Temp<-t1$y
-
 if(length(table(CTDinterp2$Sal))>0){
 s1<-approx(CTDinterp2$Depth, CTDinterp2$Sal, CTDinterp2$Depth)
 CTDinterp2$Sal<-s1$y
 }
 
+#Calculate density
 CTDinterp2$Rho<-sigmat(CTDinterp2$Temp, CTDinterp2$Sal, CTDinterp2$Pres)
 
+#Add time to the interpolations
 CTDinterp2<-CTDinterp2[order(CTDinterp2$Pres),]
-
 CTDinterp2$Year<-rep(CTDinterp2$Year[1])
 CTDinterp2$Date<-rep(CTDinterp2$Date[1])
-
 CTDinterp2<-unique(CTDinterp2)
 
+#Move data to final tables
 depths<-seq(150, 4000, 10)
-#depths<-seq(10, 50, 10)
 depths<-subset(depths, depths<max(CTDinterp2$Depth))
 diff<-(nrow(TempTable)-length(depths))
 for(d in 1:length(depths)){
 depths[d]<-which(CTDinterp2$Depth==eval(depths[d]))
 }
 CTDfinal<-CTDinterp2[c(depths),]
-
 Date<-CTDfinal$Date[1]
-
 TempTable<-cbind(TempTable, c(CTDfinal$Temp, rep(NA, eval(diff))))
 colnames(TempTable)[k+1]<-eval(Date)
 SalTable<-cbind(SalTable, c(CTDfinal$Sal, rep(NA, eval(diff))))
@@ -102,13 +107,19 @@ colnames(RhoTable)[k+1]<-eval(Date)
 
 }
 
-#Bad Salinity Values on 1989-06
+#-------------
+# Bad Data
+#-------------
+#Bad Salinity Values on 1989-06, replace with NA
 SalTable[,10]<-rep(NA)
 RhoTable[,10]<-rep(NA)
-#Bad Salinity Values on 1990-03
+#Bad Salinity Values on 1990-03, replace with NA
 SalTable[,18]<-rep(NA)
 RhoTable[,18]<-rep(NA)
 
+#----------------------------
+# Plot Profiles of CTD Data
+#----------------------------
 quartz()
 plot(TempTable[,2], TempTable$Depth*-1, type="l", xlim=c(0,22))
 last<-ncol(TempTable)-2
@@ -127,7 +138,9 @@ last<-ncol(RhoTable)-2
 for(y in 3:last){
 	lines(RhoTable[,y], RhoTable$Depth*-1)}
 
-
+#------------------------------------
+# Calculate Long-term Means of Data
+#------------------------------------
 TempTable2<-TempTable
 SalTable2<-SalTable
 RhoTable2<-RhoTable
@@ -147,12 +160,15 @@ RhoTable[,2:9]<-round(RhoTable[,2:9], digits=2)
 RhoTable[,11:17]<-round(RhoTable[,11:17], digits=2)
 RhoTable[,19:length(RhoTable)]<-round(RhoTable[,19:length(RhoTable)], digits=2)
 
-outfile<-paste("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/CTDTables_PP/BATS_CTDTemp_10m.txt", sep="")
+#--------------------------------
+# Write Processed Data to Files
+#--------------------------------
+outfile<-paste("Data/BATS/BATS_CTDTemp_10m.txt", sep="")
 write.table(TempTable, outfile, quote=FALSE, col.names=TRUE, row.names=FALSE, sep=" ")
 
-outfile<-paste("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/CTDTables_PP/BATS_CTDSal_10m.txt", sep="")
+outfile<-paste("Data/BATS/BATS_CTDSal_10m.txt", sep="")
 write.table(SalTable, outfile, quote=FALSE, col.names=TRUE, row.names=FALSE, sep=" ")
 
-outfile<-paste("/Users/kasmith/Documents/EnzymeBacteriaModel/Data/BATS/CTDTables_PP/BATS_CTDRho_10m.txt", sep="")
+outfile<-paste("Data/BATS/BATS_CTDRho_10m.txt", sep="")
 write.table(RhoTable, outfile, quote=FALSE, col.names=TRUE, row.names=FALSE, sep=" ")