diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index b84dbb45c9f52904b942bafe1a7e3d48517e1af7..a30598a4eed8e2267629488c2b405c2536f7f249 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -36,23 +36,88 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
public String name = "species A";
public Color color = Color.RED;
+
+ /**
+ * L infinity of the van Bertalanffy growth curve
+ * @unit cm
+ */
public double linfVonBert = 60.;
+
+ /**
+ * ????
+ * @unit
+ */
public double dMaxDisp = 300.;
+
+ /**
+ * length at first maturity. At that length the fish become Stage.MATURE
+ * @unit cm
+ */
public double lFirstMaturity = 40.;
+
public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
+
+ /**
+ * centile to calucale the range of species distribution
+ * @unit
+ */
public double centileForRange = 0.95;
+ /**
+ * file with the calibated parameters (from baysian approach)
+ * @unit
+ */
private String parameterSetfileName= "data/input/reality/parameterSet.csv";
+
+ /**
+ * line to use in the calibrated parameters file
+ * @unit
+ */
private int parameterSetLine =0;
+ /**
+ * year when the update of the basin should occur
+ * @unit
+ */
private long yearOfTheUpdate;
+
+ /**
+ * list of the basins to be updated
+ * column 1: name of the basin
+ * column 2: Pattractive: how the bassin become attractive (0 not attractive, 1 ??? normal weight associated to catchment size)
+ * column 3: Paccessible: how the bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
+ * @unit
+ */
private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
private String outputPath = "data/output/";
+ /**
+ * map
+ * <key> basin name
+ * <value> Duo
+ * <first> pAttractive
+ * <second> pAccessible
+ * @unit
+ */
private transient Map<String, Duo<Double, Double>> basinsToUpdate;
- private transient double kOpt; //parametre de croissance
+
+ /**
+ * growth coefficient of the von Bertalanffy growth curve (from the parameterset file)
+ * @unit year-1
+ */
+ private transient double kOpt;
+ /**
+ * minimum temperature for the reproduction (from the parameterset file)
+ * @unit °C
+ */
private transient double tempMinRep; //parametre de reproduction
+
+
+ /**
+ * list of the parameters provided by the calibration
+ * @unit
+ */
private transient List<Duo<Double, Double>> parameterSets;
public static void main(String[] args) {
@@ -65,13 +130,18 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
public double getPattractive(String basinName){
- if (basinsToUpdate.containsKey(basinName.substring(0, basinName.length()-2)))
- return basinsToUpdate.get(basinName.substring(0, basinName.length()-2)).getFirst();
+ // TODO pass in argument a Basin
+ // remove "-s" of the sea basin name
+ String shortBasinName = basinName.substring(0, basinName.length()-2);
+ if (basinsToUpdate.containsKey(shortBasinName))
+ return basinsToUpdate.get(shortBasinName).getFirst();
else
return Double.NaN;
}
public double getPaccessible(String basinName){
+ // TODO pass in argument a Basin
+ //WHY not a short name
if (basinsToUpdate.containsKey(basinName))
return basinsToUpdate.get(basinName).getSecond();
else
@@ -95,6 +165,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
InvocationTargetException {
super.initTransientParameters(pilot);
+ // basin to be updated
if ( basinsToUpdate != null){
String subDir=basinsToUpdateFile;
if (basinsToUpdateFile.lastIndexOf("/")!=-1)
@@ -186,41 +257,60 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
@Observable(description = "Nb of SI")
public int getNbSI() {
- return this.getAquaNismsList().size();
+ int nbSI = 0;
+ for (Basin basin : this.getEnvironment().getBasins() ) {
+ if (basin.getFishs(this) != null)
+ nbSI += basin.getFishs(this).size();
+ }
+ return nbSI;
}
@Observable(description = "Sizes mean of SI")
public double getSizesMeanOfSI() {
- double sum = 0;
- for (DiadromousFish list : getAquaNismsList()) {
- sum += (int) list.getAmount();
+ double totalEffective = 0;
+ double nbSI =0;
+ for (Basin basin : this.getEnvironment().getBasins() ) {
+ if (basin.getFishs(this) != null) {
+ nbSI += basin.getFishs(this).size();
+ for (DiadromousFish superFish : basin.getFishs(this)) {
+ totalEffective += superFish.getAmount();
+ }
+ }
}
- return sum / getAquaNismsList().size();
+ if (nbSI >=0)
+ return totalEffective /nbSI;
+ else
+ return Double.NaN;
}
@Observable(description = "# of SI with ind < 10")
public double getNbLittleSI() {
double nb = 0;
- for (DiadromousFish list : getAquaNismsList()) {
- if (list.getAmount() < 10) {
- nb++;
+ for (Basin basin : this.getEnvironment().getBasins() ) {
+ if (basin.getFishs(this) != null) {
+ for (DiadromousFish superFish : basin.getFishs(this)) {
+ if ( superFish.getAmount()<10L)
+ nb++;
+ }
}
}
return nb;
}
public double getMeanLengthOfMatureFish(){
- double meanLengthOfMatureFish = 0.;
double sumOfLength = 0.;
double numberOfMatureFish = 0.;
- for (DiadromousFish fish : getAquaNismsList()){
- if (fish.isMature()){
- sumOfLength += fish.getAmount() * fish.getLength();
- numberOfMatureFish += fish.getAmount();
+ for (Basin basin : this.getEnvironment().getBasins() ) {
+ if (basin.getFishs(this) != null) {
+ for (DiadromousFish fish : basin.getFishs(this)) {
+ if (fish.isMature()){
+ sumOfLength += fish.getAmount() * fish.getLength();
+ numberOfMatureFish += fish.getAmount();
+ }
+ }
}
- meanLengthOfMatureFish = sumOfLength / numberOfMatureFish;
}
- return meanLengthOfMatureFish;
+ return sumOfLength / numberOfMatureFish;
}
public double getStandardDeviationOfMatureFishLength(){
@@ -228,13 +318,18 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
double sumOfSquareLength = 0.;
double numberOfMatureFish = 0.;
double meanOfSquareLengthOfMatureFish = 0.;
- for (DiadromousFish fish : getAquaNismsList()){
- if (fish.isMature()){
- sumOfSquareLength += fish.getAmount() * Math.pow(fish.getLength(), 2);
- numberOfMatureFish += fish.getAmount();
+ for (Basin basin : this.getEnvironment().getBasins() ) {
+ if (basin.getFishs(this) != null) {
+ for (DiadromousFish fish : basin.getFishs(this)) {
+ if (fish.isMature()){
+ sumOfSquareLength += fish.getAmount() * fish.getLength() * fish.getLength();
+ numberOfMatureFish += fish.getAmount();
+ }
+ }
}
meanOfSquareLengthOfMatureFish = sumOfSquareLength / numberOfMatureFish;
- standardDeviationOfMatureFishLength = Math.pow((meanOfSquareLengthOfMatureFish - Math.pow(getMeanLengthOfMatureFish(), 2)), 0.5);
+ double meanLength = getMeanLengthOfMatureFish();
+ standardDeviationOfMatureFishLength = Math.sqrt(meanOfSquareLengthOfMatureFish - meanLength * meanLength);
}
return standardDeviationOfMatureFishLength;
}
@@ -266,29 +361,20 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
public void setlFirstMaturity(double lFirstMaturity) {
this.lFirstMaturity = lFirstMaturity;
}
-
-
- @Observable(description="Higher Populated Latitude")
- public double getHigherPopulatedLatitude() {
- double latitude = 0.0;
- RiverBasin[] basins = getEnvironment().getRiverBasins();
- int[] finalStates = getEnvironment().getFinalStates();
- for (int i = 0; i < finalStates.length; i++) {
- if ((finalStates[i] == 1) && (basins[i].getLatitude() > latitude)) {
- latitude = basins[i].getLatitude();
- }
-
- }
- return latitude;
- }
-
+
+ // ================================================================
+ // statictis for calibration
+ // ================================================================
@Observable(description="Spawners For First Time Summary Statistic")
public double computeSpawnerForFirstTimeSummaryStatistic() {
double sum = 0;
+ //TODO move TARGET to the right place
double TARGET = 5.0;
for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanAges().getMeanWithoutZero() > 0.)
- sum += Math.pow(riverBasin.getSpawnersForFirstTimeMeanAges().getMeanWithoutZero() - TARGET, 2);
+ if (riverBasin.getSpawnersForFirstTimeMeanAges().getMeanWithoutZero() > 0.) {
+ double val = riverBasin.getSpawnersForFirstTimeMeanAges().getMeanWithoutZero() - TARGET;
+ sum += val * val;
+ }
}
return sum;
}
@@ -299,6 +385,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
// 1 : read input file of observation
FileReader reader;
Scanner scanner;
+ //TODO move the obs1900 and the scanner
Map<String, Integer> obs1900 = new HashMap<String, Integer>();
try {
reader = new FileReader(fileNameInputForInitialObservation);
@@ -337,7 +424,26 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
return sumLogWhereAbs + sumLogWherePres;
}
+
+
+ // ========================================================
+ // obeserver to explore the distribution
+ // ========================================================
+ @Observable(description="Higher Populated Latitude")
+ public double getHigherPopulatedLatitude() {
+ double latitude = 0.0;
+ RiverBasin[] basins = getEnvironment().getRiverBasins();
+ int[] finalStates = getEnvironment().getFinalStates();
+ for (int i = 0; i < finalStates.length; i++) {
+ if ((finalStates[i] == 1) && (basins[i].getLatitude() > latitude)) {
+ latitude = basins[i].getLatitude();
+ }
+ }
+ return latitude;
+ }
+
+
@Observable(description="Number of colonized basins")
public double getNbColonizedBasins() {
int nb = 0;
@@ -350,6 +456,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
}
return nb;
}
+
@Observable(description="Northern colonized basins")
public double getNorthernBasins() {
@@ -364,6 +471,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
return northernBasin;
}
+
@Observable(description="Southern colonized basins")
public double getSouthernBasins() {
int southernBasin = Integer.MIN_VALUE;
@@ -408,6 +516,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
return rangeDistribution;
}
+
@Observable(description = "Range distribution")
public Double[] getRangeDistribution() {
double southernBasin = 0;
@@ -440,15 +549,23 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
return rangeDistribution;
}
- @Observable(description = "Number of fishes")
+ /**
+ * @return sum of effectives in all the river basins
+ */
+ @Observable(description = "Number of fishes in river basin")
public double getFishEffective() {
long eff = 0;
- for (DiadromousFish fish : this.getAquaNismsList()) {
- eff += fish.getAmount();
+ for (RiverBasin basin : this.getEnvironment().getRiverBasins()){
+ if (basin.getFishs(this) != null) {
+ for (DiadromousFish fish : basin.getFishs(this)) {
+ eff += fish.getAmount();
+ }
+ }
}
return eff;
}
+
@Override
public void addAquaNism(DiadromousFish fish) {
// avoid utilisation of global fishes list
@@ -456,6 +573,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
fish.getPosition().addFish(fish, this);
}
+
@Override
public void removeAquaNism(DiadromousFish fish) {
// avoid utilisation of global fishes list
@@ -463,11 +581,18 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
fish.getPosition().removeFish(fish, this);
}
+
@Override
public int compareTo(DiadromousFishGroup t) {
return name.compareTo(t.name);
}
+
+ /**
+ *
+ * concat at RngSatusIndex, temperatureCatchmentFile
+ * @return simulation name
+ */
public String getSimulationId(){
String id="_";
id=id.concat(Integer.toString(getPilot().getParameters().getRngStatusIndex()));
@@ -482,7 +607,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
public boolean isThereBasinToUpdate(){
return basinsToUpdate != null;
}
-
+
/**
* @return the outputPath
*/