add useful readme

AEDESINTER_AUTOROUTES_ADAPTIV/POSTSIMU/computeBS.edp

@@ -3,6 +3,7 @@ include "defUsedDep.edp";
  BSScore=0;
 
  indexYear=LASTYEAR-2003;
+cout<<"indexYear="<<indexYear<<endl;
  cmpData=0;
 for (int i=0;i<114;i++){
   if (useDep[i]==0)

AEDESINTER_AUTOROUTES_ADAPTIV/POSTSIMU/computeBS.sh

+rm resBS.txt
+FreeFem++-nw loopOnSimuNK.edp 2009 1
+FreeFem++-nw loopOnSimuNK.edp 2010 1
+FreeFem++-nw loopOnSimuNK.edp 2011 1
+FreeFem++-nw loopOnSimuNK.edp 2012 1
+FreeFem++-nw loopOnSimuNK.edp 2013 1
+FreeFem++-nw loopOnSimuNK.edp 2014 1
+FreeFem++-nw loopOnSimuNK.edp 2015 1
+FreeFem++-nw loopOnSimuNK.edp 2016 1
+FreeFem++-nw loopOnSimuNK.edp 2017 1
+FreeFem++-nw loopOnSimuNK.edp 2018 1
+FreeFem++-nw loopOnSimuNK.edp 2019 1
+
+FreeFem++-nw loopOnSimuNK.edp 2009 2
+FreeFem++-nw loopOnSimuNK.edp 2010 2
+FreeFem++-nw loopOnSimuNK.edp 2011 2
+FreeFem++-nw loopOnSimuNK.edp 2012 2
+FreeFem++-nw loopOnSimuNK.edp 2013 2
+FreeFem++-nw loopOnSimuNK.edp 2014 2
+FreeFem++-nw loopOnSimuNK.edp 2015 2
+FreeFem++-nw loopOnSimuNK.edp 2016 2
+FreeFem++-nw loopOnSimuNK.edp 2017 2
+FreeFem++-nw loopOnSimuNK.edp 2018 2
+
+FreeFem++-nw loopOnSimuNK.edp 2009 3
+FreeFem++-nw loopOnSimuNK.edp 2010 3
+FreeFem++-nw loopOnSimuNK.edp 2011 3
+FreeFem++-nw loopOnSimuNK.edp 2012 3
+FreeFem++-nw loopOnSimuNK.edp 2013 3
+FreeFem++-nw loopOnSimuNK.edp 2014 3
+FreeFem++-nw loopOnSimuNK.edp 2015 3
+FreeFem++-nw loopOnSimuNK.edp 2016 3
+FreeFem++-nw loopOnSimuNK.edp 2017 3
+
+FreeFem++-nw loopOnSimuNK.edp 2009 4
+FreeFem++-nw loopOnSimuNK.edp 2010 4
+FreeFem++-nw loopOnSimuNK.edp 2011 4
+FreeFem++-nw loopOnSimuNK.edp 2012 4
+FreeFem++-nw loopOnSimuNK.edp 2013 4
+FreeFem++-nw loopOnSimuNK.edp 2014 4
+FreeFem++-nw loopOnSimuNK.edp 2015 4
+FreeFem++-nw loopOnSimuNK.edp 2016 4
+
+FreeFem++-nw loopOnSimuNK.edp 2009 5
+FreeFem++-nw loopOnSimuNK.edp 2010 5
+FreeFem++-nw loopOnSimuNK.edp 2011 5
+FreeFem++-nw loopOnSimuNK.edp 2012 5
+FreeFem++-nw loopOnSimuNK.edp 2013 5
+FreeFem++-nw loopOnSimuNK.edp 2014 5
+FreeFem++-nw loopOnSimuNK.edp 2015 5
+
+FreeFem++-nw loopOnSimuNK.edp 2009 6
+FreeFem++-nw loopOnSimuNK.edp 2010 6
+FreeFem++-nw loopOnSimuNK.edp 2011 6
+FreeFem++-nw loopOnSimuNK.edp 2012 6
+FreeFem++-nw loopOnSimuNK.edp 2013 6
+FreeFem++-nw loopOnSimuNK.edp 2014 6
+
+FreeFem++-nw loopOnSimuNK.edp 2009 7
+FreeFem++-nw loopOnSimuNK.edp 2010 7
+FreeFem++-nw loopOnSimuNK.edp 2011 7
+FreeFem++-nw loopOnSimuNK.edp 2012 7
+FreeFem++-nw loopOnSimuNK.edp 2013 7
+
+FreeFem++-nw loopOnSimuNK.edp 2009 8
+FreeFem++-nw loopOnSimuNK.edp 2010 8
+FreeFem++-nw loopOnSimuNK.edp 2011 8
+FreeFem++-nw loopOnSimuNK.edp 2012 8
+
+FreeFem++-nw loopOnSimuNK.edp 2009 9
+FreeFem++-nw loopOnSimuNK.edp 2010 9
+FreeFem++-nw loopOnSimuNK.edp 2011 9
+
+FreeFem++-nw loopOnSimuNK.edp 2009 10
+FreeFem++-nw loopOnSimuNK.edp 2010 10
+
+FreeFem++-nw loopOnSimuNK.edp 2009 11
+
+
+

AEDESINTER_AUTOROUTES_ADAPTIV/POSTSIMU/meanBS.sh

+grep " 1 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' > bsModel.txt
+grep " 2 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 3 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 4 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 5 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 6 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 7 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 8 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 9 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 10 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+grep " 11 " resBS.txt | awk '{print $3}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsModel.txt
+
+
+
+grep " 1 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' > bsNull.txt
+grep " 2 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 3 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 4 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 5 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 6 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 7 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 8 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 9 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 10 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+grep " 11 " resBS.txt | awk '{print $4}' | awk 'BEGIN {FS = "|"} ; {sum+=$1} END {print sum/NR}' >> bsNull.txt
+
+
+paste -d ' ' bsModel.txt bsNull.txt > bsModelNullAux.txt
+awk '{print NR" "$0}' bsModelNullAux.txt >averageBSModelNull.txt
+
+
+
+#plot 'averageBSModelNull.txt' u 1:($2/$3) w l t "(Brier score moyen model)/(Brier score moyen null) en fonction de K"

AEDESINTER_AUTOROUTES_ADAPTIV/Readme.txt

-This file is copied during the execution of the C prog gen2speciesNL.c.
-It contains the command that must be done to allow the simulation.
+Programme pricipale FF: cas1.edp avec commentaires 
 
-This commands are necessary to run the simulation:
-1) more userFDef0.txt
-  Just to check the dynamic on each patch
-2) chmod +x genSetFunc.sh
-3) ./genSetFunc.sh
-  To generate the dynamic on each patch
+usage :
+  simulation avec assimilations: Freefem++ cas1.edp 
+  -----------------------------
+  simule sur la periode 2008--2019 en utilisant la procedure d'assimilation
+   T0 de 2008 est 1-122/365 ie 1 septembre
+   T0 de 2009-2019 est 59/365 ie 1 mars
 
+   construction de la donnee initiale
+     en 2008 la donne init est nulle, puis le 1 septembre assimilation des donnees 2008 avec thetaAssim=1
+     en y=2009 .. 2019 la donnee est contenue dans la variable w0s2d0.
+     
+     
+   Sauvegarde des oeux pour curyear ds {2008,..,2019}:
+     w1s2d(i=0)_(n=numrun)_(y=curyear) : etat des oeux a la fin de l'annee curyear
+     w0s2d(i=0)_(n=numrun)_(y=curyear) : etat des oeux ayant passe l'hiver de [dec curyear, fev curyear+1] (a utiliser pour la donnee initial de l'annee curyear+1
 
-The simuated must be ready to run:
-FreeFem++ cas1.edp
 
-Finaly, visualized with 'python vtktopng.py'
+   simulation sans assimilation: Freefem++ FIRSTYEAR NBPREDYEAR 
+   -----------------------------
+   simule sur la periode [1 fev FIRSTYEAR +(NBPREDYEAR-1), dec FIRSTYEAR +NBPREDYEAR]
+   
+      il s'agit ici de mesurer la qualite predictive du modele avec assimilation prealable simile (voir ci-dessus).
+      FIRSTYEAR ds {2009,2018}
+      NBPREDYEAR tel que FIRSTYEAR+NBPREDYEAR <= 2019  
+
+      ATTENTION: suppose que Freefem++ FIRSTYEAR NBPREDYEAR-1, avec NBPREDYEAR-1 >0 a ete joue 
+      
+
+   construction de la donnee initiale:
+     * NBPREDYEAR=1: on va chercher les oeux ayant passe l'hiver [dec FIRSTYEAR-1,fev FIRSTYEAR] lors de la simu avec assimilation, cela revient a charger w0s2d(i=0)_(n=numrun)_(FIRSTYEAR-1)
+     * NBPREDYEAR>1: on va chercher l'etat final de l'appel Freefem++ FIRSTYEAR NBPREDYEAR-1, cela revient a charger w0s2d_(NBPREDYEAR-1)_FIRSTYEAR
+
+
+   sauvegarde tout les jours simulés:
+     u2d0_NBPREDYEAR_FIRSTYEAR_rep_(n=numRun) sauvegarde des 365 jours simulé, utile pour le calcul du BS
+
+   sauvegarde en fin de simu 
+     w1s2d0_(n=numrun)_(NBPREDYEAR)_(FIRSTYEAR) : oeux diaposant en dec FIRSTYEAR +NBPREDYEAR
+     w0s2d0_(n=numrun)_(NBPREDYEAR)_(FIRSTYEAR) : oeux en fev FIRSTYEAR +NBPREDYEAR+1 ayant passe l'hiver, sera utilisé comme donnée initiale pour Freefem++ FIRSTYEAR NBPREDYEAR+1.
+
+   

AEDESINTER_AUTOROUTES_ADAPTIV/cas1.edp

@@ -29,6 +29,8 @@ if (ARGV.n>3){
   u: pop adulte
   w1: oeuf diaposant en début d'hier
   w0: oeuf ayant passe l'hiver
+
+voir Readme.txt, les commentaire ci-dessous sont obsoletes
   
   Simulation avec assimilation de 2008 a 1019
   ---------------------------------------------
@@ -43,7 +45,7 @@ if (ARGV.n>3){
      sauvegarde de w1 dans SAVE/w1s2d0_0_2008
      sauvegarde de w0 dans SAVE/w0s2d0_0_2008
   * 2009 --> 2010
-     T0 = 1 fev 2008
+     T0 = 1 fev 2009
      u=0 w1=0 ou touche pas a w0
      simulation Sauvegarde ds SAVE/u2d0_2009_rep_0
      sauvegarde de w1 dans SAVE/w1s2d0_0_2009
@@ -106,7 +108,7 @@ if (ARGV.n>3){
 int scenarioLow=0;
 int scenarioMedian=1;
 int scenarioHight=2;
-int scenario=scenarioMedian;
+int scenario=scenarioHight;
 int seed = 1234+numRun;
 int callSolver=1;
 randinit ( seed );
@@ -219,6 +221,7 @@ func real J(real[int] & u)
   cout<<"PostTrait u("<<u[0]<<","<<u[1]<<","<<u[2]<<","<<u[3]<<","<<u[4]<<","<<u[5]<<")"<<endl;
   cout<<"PostTrait J("<<D2DXu0<<","<<D2DYu0<<","<<D1Du1<<","<<R<<","<<muu1<<","<<nuu1<<","<<dirichlet0<<")"<<endl;
   include "defVarfGen.edp";
+  //Loadind w0 state
   include "defIC.edp";
   include "defIC1dNull.edp";
   include "defMatGen.edp";

AEDESINTER_AUTOROUTES_ADAPTIV/defDataAssimilation.edp

-real thetaAssim=0.5;
+real thetaAssim=1;
 //end of august
 int assimNumDay=240;