Merge pull request #14 from thiagoferreira53/GLUEP_software

GLUEP incorporated as the default system for genetic coefficient calibration using the GLUE method

.gitignore

@@ -0,0 +1,9 @@
+GLWork/
+dscsm048*
+DSSATPRO.L48
+MODEL.ERR
+DSSBatch.v48
+*.CDE
+DSCSM048.CTR
+GlueWarning.txt
+GLWork/process.txt

DSSCTR.template

@@ -0,0 +1,85 @@
+$SIMULATION_CONTROLS
+
+! A control number (CTRNO) > 0 specifies the set of controls that will be 
+! used to override the simulation controls specified in the experiment file.
+
+!-----------------------------------------------------------------------------------------
+*CONTROLS_SWITCH
+@CTRNO DESCRIPTION  
+    97 Controls for cultivar calibration using GLUE
+
+*CONTROLS
+!-----------------------------------------------------------------------------------------
+@N CONTROLS_TITLE
+97 GLUE cultivar calibration controls 
+@N GENERAL     NYERS NREPS START SDATE RSEED SNAME.................... MODEL...
+97 GE              .     .     .     .     .                           GLUEModel
+@N OPTIONS     WATER NITRO SYMBI PHOSP POTAS DISES  CHEM  TILL   CO2
+97 OP              .     .     .     .     .     .     .     .     .
+@N METHODS     WTHER INCON LIGHT EVAPO INFIL PHOTO HYDRO NSWIT MESOM MESEV MESOL METMP MEGHG
+97 ME              .     .     .     .     .     .     .     .     .     .     .     .     .
+@N MANAGEMENT  PLANT IRRIG FERTI RESID HARVS
+97 MA              .     .     .     .     .
+@N OUTPUTS     FNAME OVVEW SUMRY FROPT GROUT CAOUT WAOUT NIOUT MIOUT DIOUT VBOSE CHOUT OPOUT FMOPT
+97 OU              .     .     .     .     .     .     .     .     .     .     0     .     .     .
+
+!Definitions:
+
+!GENERAL
+! NYERS  Number of years this simulation
+! NREPS  Number of replicates (for generated weather)
+! SDATE  Start date for simulation
+! RSEED  Random number seed (for generated weather)
+! SNAME  Simulation name
+! MODEL  Crop model (e.g., MZCER046 or MZIXM046)
+
+!OPTIONS
+! WATER   Water balance and stresses simulation switch (Y=yes, N=no) 
+! NITRO   N balance and stresses simulation switch (Y=yes, N=no)
+! SYMBI   Symbiosis, N fixation simulation switch (Y=yes, N=no)
+! PHOSP   P balance and stresses simulation switch (Y=yes, N=no)
+! POTAS   K balance and stresses simulation switch (Y=yes, N=no)
+! DISES   Disease & pests simulation switch (Y=yes, N=no)
+! CHEM    Chemical applications simulation switch (not currently functional)(Y=yes, N=no)
+! TILL    Tillage events simulation switch (Y=yes, N=no)
+! CO2     CO2 data source (D = use static CO2 value from CO2046.WDA file, M = Use time series 
+!           from CO2046.WDA file, W = read from weather file header)  
+
+!METHODS
+! WTHER   Weather data source (M=measured,G=generated,S=Simmeteo,W=Wthgen)
+! INCON   Initial conditions switch (not currently used) (M=as reported, S=from previous run) 
+! LIGHT   Y=yes,N=no (not implemented)
+! EVAPO   Method of potential evapotranspiration (R=Priestley-Taylor,P=Penman FAO-24,
+!           F=FAO-56,D=Dynamic FAO-56,Z=Hourly energy balance)
+! INFIL   Mulch effects switch (R,S=SCS runoff with mulch effects, N=no mulch effects)
+! PHOTO   Photosynthesis method (C=canopy response, R=radiation use efficiency, L=leaf photosynthesis)
+! HYDRO   Hydrology method (R=Ritchie)
+! NSWIT   Nitrogen switch (experimental)
+! MESOM   Organic matter model (G=Godwin/Ceres, P=Parton/CENTURY)
+! MESEV   Soil evaporation method (S=Suleiman-Ritchie, R=Ritchie)
+! MESOL   Soil layer distribution (1=DSSAT layers, 2=no interpolation, 3=user defined)
+
+!MANAGEMENT
+! PLANT   Planting input (A=automatic planting, R=on reported date)
+! IRRIG   Irrigation input (N=no irrigation, R=reported dates, D=reported DAP, A=automatic, 
+!           F=automatic w/ fixed amounts)
+! FERTI   Fertilizer input (N=no fertilizer, R=reported dates, D=reported DAP, A=automatic
+!           F=automatic w/ fixed amounts)
+! RESID   Organic matter application (N=no residues, R=reported dates, D=reported DAP)
+! HARVS   Harvest (M=at maturity, R=reported dates, D=reported DAP, G=at specified growth stage, A=automatic)
+
+!OUTPUTS
+! FNAME   N=use defaults,Text=replacement name for output files
+! OVVEW   Overview.OUT (Y or N or E=Evaluate, but no Overview file)
+! SUMRY   Summary.OUT (Y or N)
+! FROPT   Frequency of output (days)
+! GROUT   Plant growth output (Y or N)
+! CAOUT   Carbon output (Y or N)
+! WAOUT   Water output (Y or N)
+! NIOUT   Nitrogen output (Y or N)
+! MIOUT   Phosphorus output (Y or N)
+! DIOUT   Pest and disease output (Y or N)
+! VBOSE   Verbosity (0=Summary.OUT only, N=minimal output, Y=normal output, D=detailed output)
+! CHOUT   Chemical output (not currently active (Y or N)
+! OPOUT   Management operations output (Y or N)
+! FMOPT   Output format (A=ASCII, C=CSV)

EvaluateProcessing.r

@@ -1,44 +1,47 @@
-##The program to process the data in Evaluate.Out of DSSAT output files.
-EvaluateProcessing<-function(WD, OD, CropName, RoundOfGLUE, ModelRunNumber)
-{
-
-eval(parse(text=paste("File<-readLines('",OD,"/Evaluate_output.txt',n=-1)",sep = '')));
-FileLength<-length(File);
-#print(FileLength);
-
-TitleLine = grep("@RUN",File)
-
-FrameTitle<-File[TitleLine]
-FrameData<-c();
-##Read the titles of the predictions, which is located in the 3rd line of the evaluate output.
-#FrameData<-c(); ##Creat an empty frame to store the selected data.
-
-TreatmentNumber<-(FileLength-TitleLine);##Get the number of treatments.
-#print(TreatmentNumber);
-
-SummaryFrame<-data.frame()
-
-for (j in 1:TreatmentNumber)
-{
-  n=TitleLine+j;
-  FrameData=rbind(FrameData,File[n]);##Combine the results in one matrix.
-}
-
-if(ModelRunNumber!=1)
-{
-  EvaluateFrame<-FrameData;
-  eval(parse(text = paste('write(EvaluateFrame, "',OD,'/EvaluateFrame_',
-                          RoundOfGLUE,'.txt", append = T)',sep="")));
-  #Write the data as a frame file, where repair the treatment names as an entity (" ").
-} else
-{
-  EvaluateFrame<-rbind(FrameTitle,FrameData);
-  eval(parse(text = paste('write(EvaluateFrame, "',OD,'/EvaluateFrame_',
-                          RoundOfGLUE,'.txt", append = F)',sep="")));
-}
-
-rm(File);
-}
-
-
-
+##The program to process the data in Evaluate.Out of DSSAT output files.
+EvaluateProcessing<-function(WD, OD, CropName, RoundOfGLUE, ModelRunNumber)
+{
+
+eval(parse(text=paste("File<-readLines('",OD,"/Evaluate_output.txt',n=-1)",sep = '')));
+FileLength<-length(File);
+#print(FileLength);
+
+TitleLine = grep("@RUN",File)
+
+FrameTitle<-File[TitleLine]
+FrameData<-c();
+##Read the titles of the predictions, which is located in the 3rd line of the evaluate output.
+#FrameData<-c(); ##Creat an empty frame to store the selected data.
+
+TreatmentNumber<-(FileLength-TitleLine);##Get the number of treatments.
+#print(TreatmentNumber);
+
+#SummaryFrame<-data.frame()
+
+for (j in 1:TreatmentNumber)
+{
+  n=TitleLine+j;
+  FrameData=rbind(FrameData,File[n]);##Combine the results in one matrix.
+}
+
+#The if statement had to change because it was only writing the evaluate header 
+# during the first model run -- this does not work in this parallelized version
+#if(ModelRunNumber!=1)
+if(file.exists(paste0(OD,'/EvaluateFrame_',RoundOfGLUE,'.txt')))
+{
+  EvaluateFrame<-FrameData;
+  eval(parse(text = paste('write(EvaluateFrame, "',OD,'/EvaluateFrame_',
+                          RoundOfGLUE,'.txt", append = T)',sep="")));
+  #Write the data as a frame file, where repair the treatment names as an entity (" ").
+} else
+{
+  EvaluateFrame<-rbind(FrameTitle,FrameData);
+  eval(parse(text = paste('write(EvaluateFrame, "',OD,'/EvaluateFrame_',
+                          RoundOfGLUE,'.txt", append = F)',sep="")));
+}
+
+rm(File);
+}
+
+
+