Updated the method for removing non-parameter columns on cultivar and ecotype files; Added Rye

.gitignore

@@ -6,4 +6,4 @@ DSSBatch.v48
 *.CDE
 DSCSM048.CTR
 GlueWarning.txt
-GLWork/process.txt
+GLWork/progress.txt

BatchFileSetUp.r

@@ -3,11 +3,11 @@
 BatchFileSetUp<-function(WD, OD, CultivarBatchFile)
 {
 eval(parse(text=paste('BatchFilePath="',WD,'/DSSBatch.template"',sep = '')));
-BatchFileTamplate<-readLines(BatchFilePath, n=-1);
+BatchFileTamplate<-suppressWarnings(readLines(BatchFilePath, n=-1));
 #Get the template of the batch file.
 
 eval(parse(text=paste('BatchFilePath="',OD,'/',CultivarBatchFile,'"', sep = '')));
-CultivarBatchFile<-readLines(BatchFilePath, n=-1);
+CultivarBatchFile<-suppressWarnings(readLines(BatchFilePath, n=-1));
 TotalLineNumber<-length(CultivarBatchFile);
 #Get the batch file generated with GenSelect.
 

GenotypeChange.r

@@ -1,144 +1,150 @@
-#Change the genotype file of crops in DSSAT.
-
-GenotypeChange<-function(GD, DSSATD, OD, CropName, GenotypeFileName, CultivarID, TotalParameterNumber, RunNumber, RandomMatrix, EcotypeID, EcotypeParameters)
-{
-eval(parse(text=paste('GenotypeFilePath="',GD,'/',GenotypeFileName,'.CUL"',sep = '')));
-
-ReadLine<-readLines(GenotypeFilePath, n=-1)
-GenotypeFile<-as.character(ReadLine); #Get the genotype file saved as a template.
-
-LineNumber<-grep(pattern=CultivarID, GenotypeFile); #Get the number of the line where the cultivar "GLUECUL" is located.
-OldLine<-GenotypeFile[LineNumber];#Get the line according to the line number.
-
-R<-RunNumber;#Get what parameter set will be used to change the genotype file.
-
-#check if ecotype is also being calibrated
-if(EcotypeParameters > 0){
-  eval(parse(text=paste('EcotypeFilePath="',GD,'/',GenotypeFileName,'.ECO"',sep = '')));
-
-  EcoReadLine<-readLines(EcotypeFilePath, n=-1)
-  EcotypeFile<-as.character(EcoReadLine); #Get the genotype file saved as a template.
-  EcoLineNumber<-grep(pattern=EcotypeID, EcotypeFile);
-  EcoOldLine<-EcotypeFile[EcoLineNumber];
-}
-
-# if (CropName != "SC")
-# {
-  ParameterStep<-6;
-  ValuePosition1<-(38-ParameterStep);
-  ValuePosition2<-(42-ParameterStep);
-
-  EcoValuePosition1 <- (26-ParameterStep);
-  EcoValuePosition2 <- (30-ParameterStep);
-
-  for (i in 1:TotalParameterNumber)
-  {
-  ValuePosition1<-ValuePosition1+ParameterStep;
-  ValuePosition2<-ValuePosition2+ParameterStep;
-
-  eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
-  #To solve the format problem for parameters with negative values. Modified by He, 2015-6-18.
-  if(Parameter < 0 & Parameter > -1.0)                                                          #
-  {                                                                                             #
-  ParameterFormat<-sprintf('%1.3f', Parameter);                                                 #
-  ParameterFormat<-paste(substring(ParameterFormat,1,1), substring(ParameterFormat,3), sep=''); #
-  } else if (Parameter <= -1.0 & Parameter > -10.0)                                             # 
-  {                                                                                             #
-  ParameterFormat<-sprintf('%2.2f', Parameter);                                                 #
-  } else if (Parameter <= -10.0 & Parameter > -100.0)                                           #
-  {                                                                                             #
-  ParameterFormat<-sprintf('%3.1f', Parameter);                                                 #
-  }                                                                                             #
-
-  if(Parameter >= 0 & Parameter < 10)
-  {
-  ParameterFormat<-sprintf('%1.3f', Parameter);
-  } else if (Parameter >= 10 & Parameter < 100)
-  {
-  ParameterFormat<-sprintf('%2.2f', Parameter);
-  } else if (Parameter >= 100)
-  {
-  ParameterFormat<-sprintf('%3.1f', Parameter);
-  }
-
-  if(EcotypeParameters > 0 & i > (TotalParameterNumber - EcotypeParameters)){ #Write on .ECO file
-    EcoValuePosition1 <- EcoValuePosition1+ParameterStep;
-    EcoValuePosition2 <- EcoValuePosition2+ParameterStep;
-    substr(EcoOldLine, EcoValuePosition1, EcoValuePosition2)<-ParameterFormat;
-  }else{ #Write on .CUL file
-    substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
-  }  
-  }
-  GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
-
-  if(EcotypeParameters > 0){
-    EcotypeFile[EcoLineNumber]<-EcoOldLine;#Replace the old line with new generated line in the Ecotype file.
-    eval(parse(text=paste("NewEcotypeFilePath='",OD,"/",GenotypeFileName,".ECO'",sep = '')));
-    write(EcotypeFile, file=NewEcotypeFilePath);
-    #Save the new genotype file as "eco" file in the GLWork directory.
-  }
-
-# } else
-# {
-#   ParameterStep<-15;
-# 
-#   #chp modified
-#   ValuePosition1<-(47-ParameterStep); #The initial starting point was 42, but it was changed to 46 since "EXPNO" was added by Cheryl recently.
-#   ValuePosition2<-(61-ParameterStep); #The initial ending point was 47, but it is 51 now.
-# 
-#   for (i in 1:TotalParameterNumber)
-#   {
-#   ValuePosition1<-ValuePosition1+ParameterStep;
-#   ValuePosition2<-ValuePosition2+ParameterStep;
-# 
-#   eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
-# 
-#   if(Parameter>=0 & Parameter<10)
-#   {
-#   ParameterFormat<-sprintf('%1.3f', Parameter);
-#   } else if (Parameter>=10 & Parameter<100)
-#   {
-#   ParameterFormat<-sprintf('%2.2f', Parameter);
-#   
-#   # chp added extra format statement for values between 100 and 1000
-#   } else if (Parameter>=100 & Parameter<1000)
-#   {
-#   ParameterFormat<-sprintf('%3.1f', Parameter);
-#   } else
-#   
-#   # chp - how to get format xxxx. (with nothing past the ".") ?
-#   {
-#   ParameterFormat<-sprintf('%4.0f', Parameter);
-#   }
-# 
-#   ##chp
-#   #print(ParameterFormat);
-#   #print (" ");
-#   
-#   substr(OldLine, ValuePosition1, ValuePosition2)<-'      ';# Delete initial values.
-#   substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
-#   
-#  }
-# 
-#   GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
-#   
-#   eval(parse(text=paste('ECOFilePath="',GD,'/SCCAN048.ECO"',sep = '')));
-#   ReadLine<-readLines(ECOFilePath, n=-1)
-#   ECOFile<-as.character(ReadLine);
-#   #Get the ECO file from the Genotype directory.
-#   
-#   eval(parse(text=paste("NewECOFilePath='",OD,"/SCCAN048.ECO'",sep = '')));
-#   write(ECOFile, file=NewECOFilePath);
-#   #Save the ECO file in the GLWork directory. 
-# }
-
-eval(parse(text=paste("NewGenotypeFilePath='",OD,"/",GenotypeFileName,".CUL'",sep = '')));
-write(GenotypeFile, file=NewGenotypeFilePath);
-#Save the new genotype file as "cul" file in the GLWork directory.
-
-}
-
-
-
-
-
+#Change the genotype file of crops in DSSAT.
+
+GenotypeChange<-function(GD, DSSATD, OD, CropName, GenotypeFileName, CultivarID, TotalParameterNumber, RunNumber, RandomMatrix, EcotypeID, EcotypeParameters)
+{
+eval(parse(text=paste('GenotypeFilePath="',GD,'/',GenotypeFileName,'.CUL"',sep = '')));
+
+EcoCROPGROformat <- 0
+ReadLine<-readLines(GenotypeFilePath, n=-1)
+GenotypeFile<-as.character(ReadLine); #Get the genotype file saved as a template.
+
+LineNumber<-grep(pattern=CultivarID, GenotypeFile); #Get the number of the line where the cultivar "GLUECUL" is located.
+OldLine<-GenotypeFile[LineNumber];#Get the line according to the line number.
+
+R<-RunNumber;#Get what parameter set will be used to change the genotype file.
+
+#check if ecotype is also being calibrated
+if(EcotypeParameters > 0){
+  eval(parse(text=paste('EcotypeFilePath="',GD,'/',GenotypeFileName,'.ECO"',sep = '')));
+
+  EcoReadLine<-readLines(EcotypeFilePath, n=-1)
+  EcotypeFile<-as.character(EcoReadLine); #Get the genotype file saved as a template.
+  EcoLineNumber<-grep(pattern=EcotypeID, EcotypeFile);
+  EcoOldLine<-EcotypeFile[EcoLineNumber];
+  EcoCROPGROformat <- grep(pattern="MG TM", EcotypeFile);
+}
+
+# if (CropName != "SC")
+# {
+  ParameterStep<-6;
+  ValuePosition1<-(38-ParameterStep);
+  ValuePosition2<-(42-ParameterStep);
+
+  if(length(EcoCROPGROformat) > 0){
+    EcoValuePosition1 <- (32-ParameterStep);
+    EcoValuePosition2 <- (36-ParameterStep);  
+  }else{
+    EcoValuePosition1 <- (26-ParameterStep);
+    EcoValuePosition2 <- (30-ParameterStep);
+  }
+  for (i in 1:TotalParameterNumber)
+  {
+  ValuePosition1<-ValuePosition1+ParameterStep;
+  ValuePosition2<-ValuePosition2+ParameterStep;
+
+  eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
+  #To solve the format problem for parameters with negative values. Modified by He, 2015-6-18.
+  if(Parameter < 0 & Parameter > -1.0)                                                          #
+  {                                                                                             #
+  ParameterFormat<-sprintf('%1.3f', Parameter);                                                 #
+  ParameterFormat<-paste(substring(ParameterFormat,1,1), substring(ParameterFormat,3), sep=''); #
+  } else if (Parameter <= -1.0 & Parameter > -10.0)                                             # 
+  {                                                                                             #
+  ParameterFormat<-sprintf('%2.2f', Parameter);                                                 #
+  } else if (Parameter <= -10.0 & Parameter > -100.0)                                           #
+  {                                                                                             #
+  ParameterFormat<-sprintf('%3.1f', Parameter);                                                 #
+  }                                                                                             #
+
+  if(Parameter >= 0 & Parameter < 10)
+  {
+  ParameterFormat<-sprintf('%1.3f', Parameter);
+  } else if (Parameter >= 10 & Parameter < 100)
+  {
+  ParameterFormat<-sprintf('%2.2f', Parameter);
+  } else if (Parameter >= 100)
+  {
+  ParameterFormat<-sprintf('%3.1f', Parameter);
+  }
+
+  if(EcotypeParameters > 0 & i > (TotalParameterNumber - EcotypeParameters)){ #Write on .ECO file
+    EcoValuePosition1 <- EcoValuePosition1+ParameterStep;
+    EcoValuePosition2 <- EcoValuePosition2+ParameterStep;
+    substr(EcoOldLine, EcoValuePosition1, EcoValuePosition2)<-ParameterFormat;
+  }else{ #Write on .CUL file
+    substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
+  }  
+  }
+  GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
+
+  if(EcotypeParameters > 0){
+    EcotypeFile[EcoLineNumber]<-EcoOldLine;#Replace the old line with new generated line in the Ecotype file.
+    eval(parse(text=paste("NewEcotypeFilePath='",OD,"/",GenotypeFileName,".ECO'",sep = '')));
+    write(EcotypeFile, file=NewEcotypeFilePath);
+    #Save the new genotype file as "eco" file in the GLWork directory.
+  }
+
+# } else
+# {
+#   ParameterStep<-15;
+# 
+#   #chp modified
+#   ValuePosition1<-(47-ParameterStep); #The initial starting point was 42, but it was changed to 46 since "EXPNO" was added by Cheryl recently.
+#   ValuePosition2<-(61-ParameterStep); #The initial ending point was 47, but it is 51 now.
+# 
+#   for (i in 1:TotalParameterNumber)
+#   {
+#   ValuePosition1<-ValuePosition1+ParameterStep;
+#   ValuePosition2<-ValuePosition2+ParameterStep;
+# 
+#   eval(parse(text = paste("Parameter<-RandomMatrix[R,",i,"]",sep = '')));
+# 
+#   if(Parameter>=0 & Parameter<10)
+#   {
+#   ParameterFormat<-sprintf('%1.3f', Parameter);
+#   } else if (Parameter>=10 & Parameter<100)
+#   {
+#   ParameterFormat<-sprintf('%2.2f', Parameter);
+#   
+#   # chp added extra format statement for values between 100 and 1000
+#   } else if (Parameter>=100 & Parameter<1000)
+#   {
+#   ParameterFormat<-sprintf('%3.1f', Parameter);
+#   } else
+#   
+#   # chp - how to get format xxxx. (with nothing past the ".") ?
+#   {
+#   ParameterFormat<-sprintf('%4.0f', Parameter);
+#   }
+# 
+#   ##chp
+#   #print(ParameterFormat);
+#   #print (" ");
+#   
+#   substr(OldLine, ValuePosition1, ValuePosition2)<-'      ';# Delete initial values.
+#   substr(OldLine, ValuePosition1, ValuePosition2)<-ParameterFormat;
+#   
+#  }
+# 
+#   GenotypeFile[LineNumber]<-OldLine;#Replace the old line with new generated line in the Genotype file.
+#   
+#   eval(parse(text=paste('ECOFilePath="',GD,'/SCCAN048.ECO"',sep = '')));
+#   ReadLine<-readLines(ECOFilePath, n=-1)
+#   ECOFile<-as.character(ReadLine);
+#   #Get the ECO file from the Genotype directory.
+#   
+#   eval(parse(text=paste("NewECOFilePath='",OD,"/SCCAN048.ECO'",sep = '')));
+#   write(ECOFile, file=NewECOFilePath);
+#   #Save the ECO file in the GLWork directory. 
+# }
+#print(OldLine)                                              
+eval(parse(text=paste("NewGenotypeFilePath='",OD,"/",GenotypeFileName,".CUL'",sep = '')));
+write(GenotypeFile, file=NewGenotypeFilePath);
+#Save the new genotype file as "cul" file in the GLWork directory.
+
+}
+
+
+
+
+

IntegratedLikelihoodCalculation1.r

@@ -31,7 +31,7 @@ RunNumber<-(Dimension[1]/TreatmentNumber); ##Get the number of model runs.
 ## Step 2. Get the information about measurement variance from a given Excel file.
 #library(xlsReadWrite);
 
-if (CropName=="PT" || CropName=="SC" || CropName=="CS" || CropName=="TN" || CropName=="TR" || CropName=="WH" || CropName=="PI")
+if (CropName=="PT" || CropName=="SC" || CropName=="CS" || CropName=="TN" || CropName=="TR" || CropName=="WH" || CropName=="PI" || CropName=="RY")
 {
 #  eval(parse(text=paste('VAR<-read.xls("',WD,
 #  '/MeasurementVariance.xls", sheet = "',CropName,'", rowNames = T, colNames=T)',sep = '')));
@@ -62,7 +62,7 @@ RowNames<-rownames(VAR);
 
 NumberOfMeasurement<-dim(VAR)[1];
 
-if (CropName=="BA" || CropName=="RI" || CropName=="WH" || CropName=="TF")
+if (CropName=="BA" || CropName=="RI" || CropName=="WH" || CropName=="TF" || CropName=="RY")
 {
   VAR["PD1T","Flag"]<-0;
   VAR["PWAM","Flag"]<-0;

IntegratedLikelihoodCalculation2.r

@@ -31,7 +31,7 @@ RunNumber<-(Dimension[1]/TreatmentNumber); ##Get the number of model runs.
 ## Step 2. Get the information about measurement variance from a given Excel file.
 #library(xlsReadWrite);
 
-if (CropName=="PT" || CropName=="SC" || CropName=="CS" || CropName=="TN" || CropName=="TR" || CropName=="WH" || CropName=="PI" )
+if (CropName=="PT" || CropName=="SC" || CropName=="CS" || CropName=="TN" || CropName=="TR" || CropName=="WH" || CropName=="PI" || CropName=="RY")
 {
 #  eval(parse(text=paste('VAR<-read.xls("',WD,
 #  '/MeasurementVariance.xls", sheet = "',CropName,'", rowNames = T, colNames=T)',sep = '')));
@@ -63,7 +63,7 @@ RowNames<-rownames(VAR);
 
 NumberOfMeasurement<-dim(VAR)[1];
 
-if (CropName=="BA" || CropName=="RI" || CropName=="WH" || CropName=="TF")
+if (CropName=="BA" || CropName=="RI" || CropName=="WH" || CropName=="TF" || CropName=="RY")
 {
 VAR["PD1T","Flag"]<-0;
 VAR["PWAM","Flag"]<-0;

MeasurementVariance_RY.csv

@@ -0,0 +1,10 @@
+,STD,Variance,CV,Flag,Description
+EDAP,3,9,,1,Emergence day (dap).
+ADAP,3,9,,1,Anthesis day (dap).                                  
+MDAP,7,49,,1,Physiological maturity day (dap).                   
+PD1T,4,16,,1,First pod date (YrDoy).                              
+HWAM,,,0.3,2,Yield at harvest maturity (kg [dm]/ha). 
+CWAM,,,0.3,2,Tops weight at maturity (kg [dm]/ha).  
+LAIX,,,0.4,2,"Leaf area index, maximum."
+HWUM,,,0.1,2,Grain unit weight at maturity (g/seed)
+L.SM,3,9,,2,"Leaf number per stem at maturity. The symbol ""#"" was changed to ""."", since it is the symbol of comments in R."

ModelRun.r

@@ -65,7 +65,7 @@ pbapply_custom <- function (X, FUN, ..., cl = NULL)
         rval[i] <- list(PAR_FUN(cl, X[Split[[i]]], FUN, 
                                 ...))
         setpb(pb, i)
-        write.table(i/B*100,file = paste0(OD,'process.txt'), row.names = FALSE, col.names = FALSE)
+        write.table(i/B*100,file = paste0(OD,'progress.txt'), row.names = FALSE, col.names = FALSE)
       }
     }
     else if (identical(cl, "future")) {