diff --git a/.gitignore b/.gitignore
index 9df0b0a4dd67f79820163b21d78bbb182ada440a..08b864ff2aee1974c9e26cc538148ea45f9ad5a9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -100,29 +100,31 @@ target
 .classpath
 .project
 org.*
+
+/src/main/java/environment/*.ucls
+/src/main/java/environment/TestShape.java
+/src/main/java/species/testAlea.java
+/src/main/java/species/Essai.java
 /src/main/java/miscellaneous/Essai.java
->>>>>>> master
-/exploration/R/.Rhistory
-/exploration/R/.RData
+
 /outcmaesaxlen.dat
 /outcmaesdisp.dat
 /outcmaesfit.dat
 /outcmaesstddev.dat
 /outcmaesxmean.dat
 /outcmaesxrecentbest.dat
-/exploration/scriptR/BruchPrg.R.orig
-.Rproj.user
-/exploration/scriptR/.RData
-/exploration/scriptR/*.Rproj
-/exploration/scriptR/.Rhistory
-/exploration/scriptR/scriptR.Rproj
-/exploration/scriptR/.Rproj.user/
-/exploration/scriptR/.RData
-/src/main/java/environment/*.ucls
-/src/main/java/environment/TestShape.java
-/src/main/java/species/testAlea.java
-/data/input/northeastamerica/shape/*.qix
-/src/main/java/species/Essai.java
-/exploration/GR3D_Rdescription/.RData
-/exploration/GR3D_Rdescription/.Rhistory
-/exploration/GR3D_Rdescription/.~lock.*
+
+# R: files
+*.Rproj
+*.Rhistory
+*.RData
+*.Rproj.user
+*.~lock.*
+
+# qgis file
+*.qix
+
+
+
+
+
diff --git a/data/input/northeastamerica/RIO_obs_empty.xml b/data/input/northeastamerica/RIO_obs_empty.xml
index 8f9e49df048a13acbfb5b651087d5e828b063d6b..3ee9b0dd6e3b5b6acc79d254dceb396d9fc16db3 100644
--- a/data/input/northeastamerica/RIO_obs_empty.xml
+++ b/data/input/northeastamerica/RIO_obs_empty.xml
@@ -1,150 +1,3 @@
 <hashtable>
-	<entry>
-		<!--
-		
-		<java-class>fr.cemagref.simaqualife.kernel.AquaticWorld</java-class>-->
-		<java-class>environment.RIOBasinNetworkWithContinent</java-class>
 	
-		<fr.cemagref.observation.kernel.ObservablesHandler>
-			<observers>
-				<environment.RIOBasinNetworkObserverWithContinent>
-					<title>North East America</title>
-					<threshold>1000000</threshold>
-					<colorScaleEnum>RedsScale</colorScaleEnum>
-				</environment.RIOBasinNetworkObserverWithContinent>
-
-				<environment.RIOBasinNetworkObserverPresence>
-					<title>Shad presence in North East America</title>
-					<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
-					<period>obs_1900_1950</period>
-				</environment.RIOBasinNetworkObserverPresence>
-			</observers>
-		</fr.cemagref.observation.kernel.ObservablesHandler>
-	</entry>
-	<entry>
-		<java-class>species.DiadromousFishGroup</java-class>
-		<fr.cemagref.observation.kernel.ObservablesHandler>
-			<observers>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Number of colonized
-						basins
-					</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>number of basins</yAxisLabel>
-					<variableName>getNbColonizedBasins</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Total Abundance</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>number of fishes</yAxisLabel>
-					<variableName>getFishEffective</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Abundance of spawners</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>number
-						of fishes
-					</yAxisLabel>
-					<variableName>getSpawnerEffective</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Abundance of male spawners</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>number of fishes</yAxisLabel>
-					<variableName>getMaleSpawnerEffective</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Abundance of female spawners</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>number
-						of fishes
-					</yAxisLabel>
-					<variableName>getFemaleSpawnerEffective</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<observer.TemporalRangeSerieChart>
-					<title>Range distribution</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>latitude</yAxisLabel>
-					<variableName>getRangeDistributionWithLat</variableName>
-				</observer.TemporalRangeSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Mean age at first reproduction for female</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>age (year)</yAxisLabel>
-					<variableName>getMeanAgeOfFirstReprodutionForFemale</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Mean age at first reproduction
-						for male
-					</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>age (year)</yAxisLabel>
-					<variableName>getMeanAgeOfFirstReprodutionForMale</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Statistic for male spawners age</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel></yAxisLabel>
-					<variableName>computeMaleSpawnerForFirstTimeSummaryStatistic</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Statistic for female
-						spawners age
-					</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel></yAxisLabel>
-					<variableName>computeFemaleSpawnerForFirstTimeSummaryStatistic</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Mean length at first reproduction for female</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>length (cm)</yAxisLabel>
-					<variableName>getMeanLengthOfFirstReprodutionForFemale</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-				<fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-					<graphType>LINE</graphType>
-					<title>Mean length at first
-						reproduction for male
-					</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>length (cm)</yAxisLabel>
-					<variableName>getMeanLengthOfFirstReprodutionForMale</variableName>
-				</fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-			</observers>
-		</fr.cemagref.observation.kernel.ObservablesHandler>
-	</entry>
-	<entry>
-		<java-class>environment.RiverBasin</java-class>
-		<fr.cemagref.observation.kernel.ObservablesHandler>
-			<observers>
-				<observer.TemporalSerieChartForBasin>
-					<graphType>LINE</graphType>
-					<title>Number of juveniles</title>
-					<xAxisLabel>Time
-						(season)
-					</xAxisLabel>
-					<yAxisLabel>number of juveniles</yAxisLabel>
-					<variableName>getJuvenileNumber</variableName>
-				</observer.TemporalSerieChartForBasin>
-				<observer.TemporalSerieChartForBasin>
-					<graphType>LINE</graphType>
-					<title>% Autochtone</title>
-					<xAxisLabel>Time (season)</xAxisLabel>
-					<yAxisLabel>% Autochtone</yAxisLabel>
-					<variableName>getLastPercentageOfAutochtone</variableName>
-				</observer.TemporalSerieChartForBasin>
-			</observers>
-		</fr.cemagref.observation.kernel.ObservablesHandler>
-	</entry>
-
 </hashtable>
\ No newline at end of file
diff --git a/exploration/R_AS_GR3D/tryFromRougier.R b/exploration/R_AS_GR3D/tryFromRougier.R
index 349ad0160b637ab181a427a07e0fa5187b65ade6..e793ccb627bd3f231484e73bd449734e3a37c152 100644
--- a/exploration/R_AS_GR3D/tryFromRougier.R
+++ b/exploration/R_AS_GR3D/tryFromRougier.R
@@ -6,22 +6,25 @@ rm(list=ls())
 
 set.seed(1)
 
-# parameters and prios=rs of parameters to be fitted
-inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
-# load prior
-prior = list()
-for (i in 1:length(inputData$parameters)) {
-  p = inputData$parameters[[i]]
-  prior[[i]] = unlist(p$prior)
-}
-
-parametersNames = list()
-for (i in 1:length(inputData$parameters)) {
-  parametersNames = c(parametersNames, inputData$parameters[[i]]$javapath)
-}
-
-
-thetas = c(0.45, 10.5)
+# # parameters and prios=rs of parameters to be fitted
+# inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
+# # load prior
+# prior = list()
+# for (i in 1:length(inputData$parameters)) {
+#   p = inputData$parameters[[i]]
+#   prior[[i]] = unlist(p$prior)
+# }
+# 
+# parametersNames = list()
+# for (i in 1:length(inputData$parameters)) {
+#   parametersNames = c(parametersNames, inputData$parameters[[i]]$javapath)
+# }
+# parametersNames = unlist(parametersNames)
+
+parametersNames = c("processes.processesEachStep.8.tempMinRep",
+                "processes.processesEachStep.8.ratioS95_S50",
+                "processes.processesEachStep.6.pHomingAfterEquil")
+thetas = c(10, 2, 0.7)
 
 # path to outputs
 outputDir = "simus/"
@@ -33,19 +36,26 @@ timeStepDuration =1
 
 seed = 1
 
+## to have the same working diretory as GR3D
+setwd("../..")
 
-
-arguments = c('-d','-simDuration',simDuration, '-simBegin',simBegin,
+arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
             '-timeStepDuration',timeStepDuration, 
             '-RNGStatusIndex', format(seed,scientific = FALSE),
-            '-groups',"../../data/input/northeastamerica/fishRIOBasin_Sapidissima_PL.xml",
-            '-env',"../../data/input/northeastamerica/RIOBNneaBasins.xml",
-            '-observers',"../../data/input/northeastamerica/RIO_obs_empty.xml")
+            '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
+            '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
+            '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
 
 outputFile = paste0(outputDir,"output",seed)
 
 .jinit(classpath = jarfile, force.init = TRUE)
-.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(unlist(parametersNames)),.jarray(thetas))
+.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(parametersNames),.jarray(thetas))
+
+
+
+
+
+
 
 # return a function to run the model with parameters as arguments
 salrun <- function(jarfile, simDuration, simBegin, timeStepDuration = 1) {