diff --git a/src/main/java/analysis/ExportSpeciesRange.java b/src/main/java/analysis/ExportSpeciesRange.java
index f9ca25e32ea39e137681c74efa449fa160c21122..5f4bcfa1d98de8976bb894d1031bcc0bfb2d7fa9 100644
--- a/src/main/java/analysis/ExportSpeciesRange.java
+++ b/src/main/java/analysis/ExportSpeciesRange.java
@@ -27,74 +27,135 @@ import java.io.IOException;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
+import environment.RiverBasin;
import environment.Time;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot;
+import miscellaneous.TreeMapForCentile;
import species.DiadromousFish;
import species.DiadromousFishGroup;
/**
*
*/
+@Deprecated
public class ExportSpeciesRange extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
-
private String fileNameOutput = "range";
+ /**
+ * centile to calculate the nothernmost range of species distribution
+ *
+ * @unit
+ */
+ public double centileForRange = 0.95;
+
private transient BufferedWriter bW;
- private transient String sep=";";
+ private transient String sep = ";";
public static void main(String[] args) {
- System.out.println((new XStream(new DomDriver()))
- .toXML(new ExportSpeciesRange()));
+ System.out.println((new XStream(new DomDriver())).toXML(new ExportSpeciesRange()));
}
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.
+ * pilot.Pilot)
*/
@Override
public void initTransientParameters(Pilot pilot) {
super.initTransientParameters(pilot);
- sep=";";
+ sep = ";";
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
*/
@Override
public void doProcess(DiadromousFishGroup group) {
-
- if (bW==null){
- if (fileNameOutput != null){
- new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+
+ if (bW == null) {
+ if (fileNameOutput != null) {
+ new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
try {
- bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
- fileNameOutput +group.getSimulationId()+ ".csv")));
+ bW = new BufferedWriter(
+ new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
- bW.write("timestep"+sep+"year"+sep+"season"+sep+"medianRange"
- +sep+"southRange"+sep+"northRange"+sep+"centileRange"+"\n");
+ bW.write("timestep" + sep + "year" + sep + "season" + sep + "medianRange" + sep + "southRange" + sep
+ + "northRange" + sep + "centileRange" + "\n");
} catch (IOException e) {
e.printStackTrace();
}
}
}
-
+
try {
Time time = group.getEnvironment().getTime();
- bW.write(group.getPilot().getCurrentTime()+sep+time.getYear(group.getPilot()));
- bW.write(sep+time.getSeason(group.getPilot()));
-
- for (double value : group.getRangeDistributionWithLat()){
- bW.write(sep+value);
+ bW.write(group.getPilot().getCurrentTime() + sep + time.getYear(group.getPilot()));
+ bW.write(sep + time.getSeason(group.getPilot()));
+
+ for (double value : getRangeSpawnerDistributionWithLat(group)) {
+ bW.write(sep + value);
}
bW.write("\n");
-
- if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1){
+
+ if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration() - 1) {
bW.close();
}
} catch (IOException e) {
e.printStackTrace();
}
}
+
+
+ private Double[] getRangeSpawnerDistributionWithLat(DiadromousFishGroup group) {
+
+ TreeMapForCentile latitudeEffective = new TreeMapForCentile();
+ double southernLatitude = 90.;
+ double northernLatitude = 0.;
+
+ // loop over riverBasin
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ long effective = (long) (riverBasin.getLastFemaleSpawnerNumber() + riverBasin.getLastMaleSpawnerNumber());
+
+ if (effective > 0) {
+ latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
+ if (riverBasin.getLatitude() < southernLatitude)
+ southernLatitude = riverBasin.getLatitude();
+ if (riverBasin.getLatitude() > northernLatitude)
+ northernLatitude = riverBasin.getLatitude();
+ }
+ }
+
+ // compute result
+ // (y, y-low, y-high) data item
+ Double[] rangeDistribution = new Double[4];
+ if (!latitudeEffective.isEmpty()) {
+ // median
+ rangeDistribution[0] = latitudeEffective.calculateMedian();
+ // southern
+ rangeDistribution[1] = southernLatitude;
+ // northern
+ rangeDistribution[2] = northernLatitude;
+ // centile
+ rangeDistribution[3] = latitudeEffective.calculateCentile(centileForRange);
+ } else {
+ // median
+ rangeDistribution[0] = (southernLatitude + northernLatitude) / 2.;
+ // southern
+ rangeDistribution[1] = rangeDistribution[0];
+ // northern
+ rangeDistribution[2] = rangeDistribution[0];
+ // centile
+ rangeDistribution[3] = rangeDistribution[0];
+ }
+ return rangeDistribution;
+ }
}
diff --git a/src/main/java/analysis/TypeTrajectoryCV.java b/src/main/java/analysis/TypeTrajectoryCV.java
index c76340cf5746a44fea5df49a358e5aad980f0ee3..a90fb6ce02d0bb843a120a535815153ceb8f6929 100644
--- a/src/main/java/analysis/TypeTrajectoryCV.java
+++ b/src/main/java/analysis/TypeTrajectoryCV.java
@@ -1,11 +1,5 @@
package analysis;
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import species.DiadromousFish;
-import species.DiadromousFishGroup;
-
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
@@ -15,208 +9,355 @@ import java.util.HashMap;
import java.util.Locale;
import java.util.Map;
import java.util.Scanner;
+import java.util.TreeMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import environment.RIOBasinNetwork;
+import environment.RiverBasin;
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFish.Gender;
+import species.DiadromousFishGroup;
+
public class TypeTrajectoryCV extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
- private String fileNameOutput = "summary";
- private transient BufferedWriter bW;
-
- public static void main(String[] args) {
- System.out.println((new XStream(new DomDriver())).toXML(new TypeTrajectoryCV()));
-
- //TypeTrajectoryCV trajectoryCV = new TypeTrajectoryCV();
-// trajectoryCV.computeKapa("data/input/reality/Obs1900.csv");
- }
-
- @Override
- public void doProcess(DiadromousFishGroup group) {
-
- // int[] finalStates = group.getEnvironment().getFinalStates();
- // int[] finalStatesWithStoch = group.getEnvironment().getFinalStatesWithStochasticity();
- int[] finalStatesForKappa = group.getEnvironment().getFinalStatesForKappa();
- double[] geoMeanRecOverProdCap = group.getEnvironment().getGeoMeansLastRecsOverProdCaps();
- double[] meanLastRec = group.getEnvironment().getMeanLastRecruitments();
- double[] meanPercOfAut = group.getEnvironment().getMeanLastPercOfAut();
- double[] probOfNonNulRecruitmentDuringLastYears = group.getEnvironment().getProbOfNonNulRecruitmentDuringLastYears();
- long[] yearsOfFirstNonNulRep = group.getEnvironment().getYearsOfFirstNonNulRep();
- long[] yearsOfLastNulRep = group.getEnvironment().getYearsOfLastNulRep();
- String[] finalStatesNames = group.getEnvironment().getRiverBasinNames();
- double[] finalProbabilityOfPresence = group.getEnvironment().getFinalProbabilityOfPresence();
-
- // System.out.println(group.getEnvironment().getMeanLastRecruitmentsBV2());
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "final states : " + Arrays.toString(finalStates));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "final states wirth stoch : " + Arrays.toString(finalStatesWithStoch));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "geo mean of last 10 years R/alpha : " + Arrays.toString(geoMeanRecOverProdCap));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "mean last recruitment : " + Arrays.toString(meanLastRec));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "prob non nul rec : " + Arrays.toString(probOfNonNulRecruitmentDuringLastYears));
- //System.out.println("mean last percentage of autochtone : " + Arrays.toString(meanPercOfAut));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "year of first non nul reproduction : " + Arrays.toString(yearsOfFirstNonNulRep));
- //System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "year of last nul reproduction : " + Arrays.toString(yearsOfLastNulRep));
- //this.fireChangesToObservers();
- if (fileNameOutput != null) {
- // create the subdirectorrys if necessary ?
- new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
-
- try {
- bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
- fileNameOutput+group.getSimulationId()+ ".csv")));
- int nbBV = finalStatesNames.length;
-
- bW.write("nom des bv");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + finalStatesNames[i]);
- }
- bW.write("\n");
-
- bW.write("Final states");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + finalStatesForKappa[i]);
- }
- bW.write("\n");
-
- bW.write("year of first non nul reproduction");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + yearsOfFirstNonNulRep[i]);
- }
- bW.write("\n");
-
- bW.write("year of last nul reproduction");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + yearsOfLastNulRep[i]);
- }
- bW.write("\n");
-
- bW.write("mean last recruitment");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + meanLastRec[i]);
- }
- bW.write("\n");
-
- bW.write("geo mean of last 10 years R/alpha");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + geoMeanRecOverProdCap[i]);
- }
- bW.write("\n");
-
- bW.write("mean last percentage of autochtone");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + meanPercOfAut[i]);
- }
- bW.write("\n");
-
- bW.write("prob of non nul recruitment during last years");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + probOfNonNulRecruitmentDuringLastYears[i]);
- }
- bW.write("\n");
-
- computeKapa(bW, "data/input/reality/Obs1900.csv", finalStatesForKappa, finalStatesNames);
- bW.write("\n");
-
- bW.write("likelihood;" + ((Double) group.computeLikelihood()).toString() + "\n");
-
- bW.write("spawnersMatureAgeSumStat;" + group.computeFemaleSpawnerForFirstTimeSummaryStatistic() + "\n");
-
- bW.write("higherPopulatedLatitude;" + group.getHigherPopulatedLatitude() + "\n");
-
- bW.write("graine;" + group.getPilot().getParameters().getRngStatusIndex() + "\n");
-
- bW.write("finalProbOfPres");
- for (int i = 0; i < nbBV; i++) {
- bW.write(";" + finalProbabilityOfPresence[i]);
- }
- bW.close();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
- }
-
- public void computeKapa(BufferedWriter writer, String fileNameInputForInitialObservation, int[] finalStatesForKappa, String[] finalStatesNames) throws IOException {
-
- // 1 : read input file of observation
- FileReader reader;
- Scanner scanner;
- Map<String, Integer> obs1900 = new HashMap<String, Integer>();
- try {
- reader = new FileReader(fileNameInputForInitialObservation);
- // Parsing the file
- scanner = new Scanner(reader);
- scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
- scanner.useDelimiter(Pattern.compile("[;\r]"));
-
- scanner.nextLine(); // to skip the file first line of entete
-
- while (scanner.hasNext()) {
- obs1900.put(scanner.next().replaceAll("\n", ""), scanner.nextInt());
- }
- reader.close();
-
- } catch (IOException ex) {
- Logger.getLogger(TypeTrajectoryCV.class.getName()).log(Level.SEVERE, null, ex);
- }
-
- // 2 : compute the confusion matrix between observed and computed data
- // obs 0 1
- // pred 0 VN FN
- // 1 FP VP
- double[][] confusionMatrix = new double[2][2];
- int computedVal;
- int obsVal;
- int nbVal = 0;
- for (int i = 0; i < finalStatesNames.length; i++) {
- if (obs1900.containsKey(finalStatesNames[i])) {
- computedVal = (finalStatesForKappa[i] > 0) ? 1 : 0;
- obsVal = obs1900.get(finalStatesNames[i]);
- if (computedVal == 0) {
- if (obsVal == 0) {
- confusionMatrix[0][0]++;
- } else {
- confusionMatrix[0][1]++;
- }
- } else {
- if (obsVal == 0) {
- confusionMatrix[1][0]++;
- } else {
- confusionMatrix[1][1]++;
- }
- }
- nbVal++;
- }
- }
- // normalisation
- confusionMatrix[0][0] = confusionMatrix[0][0] / nbVal;
- confusionMatrix[0][1] = confusionMatrix[0][1] / nbVal;
- confusionMatrix[1][0] = confusionMatrix[1][0] / nbVal;
- confusionMatrix[1][1] = confusionMatrix[1][1] / nbVal;
-
- // 3 compute kapa
- // kapa= (pra-pre)/(1-pre)
- // with pra=VN+VP and pre=(VN+FN)*(VN+FP)+(FN+VP)*(FP+VP)
- double VN = confusionMatrix[0][0];
- double FN = confusionMatrix[0][1];
- double FP = confusionMatrix[1][0];
- double VP = confusionMatrix[1][1];
- double pra = VN + VP;
- double pre = (VN + FN) * (VN + FP) + (FN + VP) * (FP + VP);
- double kapa = (pra - pre) / (1 - pre);
-
- writer.write("confusion matrix(VN,FN,FP,VP);");
- writer.write(((Double) confusionMatrix[0][0]).toString());
- writer.write(";");
- writer.write(((Double) confusionMatrix[0][1]).toString());
- writer.write(";");
- writer.write(((Double) confusionMatrix[1][0]).toString());
- writer.write(";");
- writer.write(((Double) confusionMatrix[1][1]).toString());
- writer.write("\nkappa;");
- writer.write(((Double) kapa).toString());
-
- //System.out.println("kappa value: " + kapa);
- }
+ private String fileNameOutput = "summary";
+
+ private String presenceFileName = "data/input/northeastamerica/nea_presence.csv";
+ private String period = "obs_1751_1850";
+
+ private Double targetedAgeForFemaleSpawnerForFirstTime = 5.5;
+ private Double targetedAgeForMaleSpawnerForFirstTime = 4.5;
+
+ /**
+ * The minimum number of recruits to consider a basin as populated
+ *
+ * @unit: #
+ */
+ private int minimumRecruitsForPopulatedBasin = 50;
+
+ private transient Map<String, Map<String, Integer>> presences;
+
+ private transient BufferedWriter bW;
+
+ public static void main(String[] args) {
+ System.out.println((new XStream(new DomDriver())).toXML(new TypeTrajectoryCV()));
+
+ // TypeTrajectoryCV trajectoryCV = new TypeTrajectoryCV();
+ // trajectoryCV.computeKapa("data/input/reality/Obs1900.csv");
+ }
+
+
+ @Override
+ public void initTransientParameters(Pilot pilot) {
+ super.initTransientParameters(pilot);
+ // read the file of presence in river basin
+ try {
+ // open the file
+ FileReader reader = new FileReader(presenceFileName);
+ // Parsing the file
+ Scanner scanner = new Scanner(reader);
+ scanner.useLocale(Locale.ENGLISH); // to have a point as decimal
+ // separator !!!
+ // scanner.useDelimiter(Pattern.compile("[;,\r\n]"));
+
+ // read the headers
+ String[] headers = scanner.nextLine().split(",");
+ presences = new TreeMap<String, Map<String, Integer>>();
+ boolean periodTest = false;
+ for (int i = 2; i < headers.length; i++) {
+ if (period.equals(headers[i]))
+ periodTest = true;
+ presences.put(headers[i], new TreeMap<String, Integer>());
+ }
+
+ // TODO send the error
+ if (periodTest == false)
+ System.out.println("The period " + period + " is not present in the file " + presenceFileName);
+ // read the lines
+ while (scanner.hasNextLine()) {
+ String[] fields = scanner.nextLine().split(",");
+ // System.out.println(Arrays.toString(fields));
+
+ for (int j = 2; j < headers.length; j++) {
+ if (j >= fields.length)
+ presences.get(headers[j]).put(fields[1], -1);
+ else {
+ if (fields[j].compareTo("") == 0)
+ presences.get(headers[j]).put(fields[1], -1);
+ else
+ presences.get(headers[j]).put(fields[1], Integer.valueOf(fields[j]));
+ }
+ }
+ }
+ reader.close();
+ scanner.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ @Override
+ public void doProcess(DiadromousFishGroup group) {
+
+ // int[] finalStates = group.getEnvironment().getFinalStates();
+ // int[] finalStatesWithStoch = group.getEnvironment().getFinalStatesWithStochasticity();
+ int[] finalStatesForKappa = group.getEnvironment().getFinalStatesForKappa();
+ double[] geoMeanRecOverProdCap = group.getEnvironment().getGeoMeansLastRecsOverProdCaps();
+ double[] meanLastRec = group.getEnvironment().getMeanLastRecruitments();
+ double[] meanPercOfAut = group.getEnvironment().getMeanLastPercOfAut();
+ double[] probOfNonNulRecruitmentDuringLastYears = group.getEnvironment().getProbOfNonNulRecruitmentDuringLastYears();
+ long[] yearsOfFirstNonNulRep = group.getEnvironment().getYearsOfFirstNonNulRep();
+ long[] yearsOfLastNulRep = group.getEnvironment().getYearsOfLastNulRep();
+ String[] finalStatesNames = group.getEnvironment().getRiverBasinNames();
+ double[] finalProbabilityOfPresence = group.getEnvironment().getFinalProbabilityOfPresence();
+
+ // System.out.println(group.getEnvironment().getMeanLastRecruitmentsBV2());
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "final states : " +
+ // Arrays.toString(finalStates));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "final states wirth stoch : " +
+ // Arrays.toString(finalStatesWithStoch));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "geo mean of last 10 years
+ // R/alpha : " + Arrays.toString(geoMeanRecOverProdCap));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "mean last recruitment : " +
+ // Arrays.toString(meanLastRec));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "prob non nul rec : " +
+ // Arrays.toString(probOfNonNulRecruitmentDuringLastYears));
+ // System.out.println("mean last percentage of autochtone : " + Arrays.toString(meanPercOfAut));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "year of first non nul
+ // reproduction : " + Arrays.toString(yearsOfFirstNonNulRep));
+ // System.out.println(" nom des bv " + Arrays.deepToString(finalStatesNames) + "year of last nul reproduction :
+ // " + Arrays.toString(yearsOfLastNulRep));
+ // this.fireChangesToObservers();
+ if (fileNameOutput != null) {
+ // create the subdirectorrys if necessary ?
+ new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
+
+ try {
+ bW = new BufferedWriter(
+ new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+ int nbBV = finalStatesNames.length;
+
+ bW.write("nom des bv");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + finalStatesNames[i]);
+ }
+ bW.write("\n");
+
+ bW.write("Final states");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + finalStatesForKappa[i]);
+ }
+ bW.write("\n");
+
+ bW.write("year of first non nul reproduction");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + yearsOfFirstNonNulRep[i]);
+ }
+ bW.write("\n");
+
+ bW.write("year of last nul reproduction");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + yearsOfLastNulRep[i]);
+ }
+ bW.write("\n");
+
+ bW.write("mean last recruitment");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + meanLastRec[i]);
+ }
+ bW.write("\n");
+
+ bW.write("geo mean of last 10 years R/alpha");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + geoMeanRecOverProdCap[i]);
+ }
+ bW.write("\n");
+
+ bW.write("mean last percentage of autochtone");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + meanPercOfAut[i]);
+ }
+ bW.write("\n");
+
+ bW.write("prob of non nul recruitment during last years");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + probOfNonNulRecruitmentDuringLastYears[i]);
+ }
+ bW.write("\n");
+
+ computeKapa(bW, "data/input/reality/Obs1900.csv", finalStatesForKappa, finalStatesNames);
+ bW.write("\n");
+
+ bW.write("likelihood;" + ((Double) computeLikelihood(group)).toString() + "\n");
+
+ bW.write("spawnersMatureAgeSumStat;" + computeFemaleSpawnerForFirstTimeSummaryStatistic(group) + "\n");
+
+ bW.write("higherPopulatedLatitude;" + getNorthernmostPopulatedLatitude(group) + "\n");
+
+ bW.write("graine;" + group.getPilot().getParameters().getRngStatusIndex() + "\n");
+
+ bW.write("finalProbOfPres");
+ for (int i = 0; i < nbBV; i++) {
+ bW.write(";" + finalProbabilityOfPresence[i]);
+ }
+ bW.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+ public void computeKapa(BufferedWriter writer, String fileNameInputForInitialObservation, int[] finalStatesForKappa,
+ String[] finalStatesNames) throws IOException {
+
+ // 1 : read input file of observation
+ FileReader reader;
+ Scanner scanner;
+ Map<String, Integer> obs1900 = new HashMap<String, Integer>();
+ try {
+ reader = new FileReader(fileNameInputForInitialObservation);
+ // Parsing the file
+ scanner = new Scanner(reader);
+ scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
+ scanner.useDelimiter(Pattern.compile("[;\r]"));
+
+ scanner.nextLine(); // to skip the file first line of entete
+
+ while (scanner.hasNext()) {
+ obs1900.put(scanner.next().replaceAll("\n", ""), scanner.nextInt());
+ }
+ reader.close();
+
+ } catch (IOException ex) {
+ Logger.getLogger(TypeTrajectoryCV.class.getName()).log(Level.SEVERE, null, ex);
+ }
+
+ // 2 : compute the confusion matrix between observed and computed data
+ // obs 0 1
+ // pred 0 VN FN
+ // 1 FP VP
+ double[][] confusionMatrix = new double[2][2];
+ int computedVal;
+ int obsVal;
+ int nbVal = 0;
+ for (int i = 0; i < finalStatesNames.length; i++) {
+ if (obs1900.containsKey(finalStatesNames[i])) {
+ computedVal = (finalStatesForKappa[i] > 0) ? 1 : 0;
+ obsVal = obs1900.get(finalStatesNames[i]);
+ if (computedVal == 0) {
+ if (obsVal == 0) {
+ confusionMatrix[0][0]++;
+ } else {
+ confusionMatrix[0][1]++;
+ }
+ } else {
+ if (obsVal == 0) {
+ confusionMatrix[1][0]++;
+ } else {
+ confusionMatrix[1][1]++;
+ }
+ }
+ nbVal++;
+ }
+ }
+ // normalisation
+ confusionMatrix[0][0] = confusionMatrix[0][0] / nbVal;
+ confusionMatrix[0][1] = confusionMatrix[0][1] / nbVal;
+ confusionMatrix[1][0] = confusionMatrix[1][0] / nbVal;
+ confusionMatrix[1][1] = confusionMatrix[1][1] / nbVal;
+
+ // 3 compute kapa
+ // kapa= (pra-pre)/(1-pre)
+ // with pra=VN+VP and pre=(VN+FN)*(VN+FP)+(FN+VP)*(FP+VP)
+ double VN = confusionMatrix[0][0];
+ double FN = confusionMatrix[0][1];
+ double FP = confusionMatrix[1][0];
+ double VP = confusionMatrix[1][1];
+ double pra = VN + VP;
+ double pre = (VN + FN) * (VN + FP) + (FN + VP) * (FP + VP);
+ double kapa = (pra - pre) / (1 - pre);
+
+ writer.write("confusion matrix(VN,FN,FP,VP);");
+ writer.write(((Double) confusionMatrix[0][0]).toString());
+ writer.write(";");
+ writer.write(((Double) confusionMatrix[0][1]).toString());
+ writer.write(";");
+ writer.write(((Double) confusionMatrix[1][0]).toString());
+ writer.write(";");
+ writer.write(((Double) confusionMatrix[1][1]).toString());
+ writer.write("\nkappa;");
+ writer.write(((Double) kapa).toString());
+
+ // System.out.println("kappa value: " + kapa);
+ }
+
+
+ public double computeLikelihood(DiadromousFishGroup group) {
+ int obsVal;
+ double sumLogWherePres = 0.;
+ double sumLogWhereAbs = 0.;
+ RIOBasinNetwork rioBasinNetwork = group.getEnvironment();
+ final double[] probOfNonNulRecruitmentDuringLastYears = rioBasinNetwork.getProbOfNonNulRecruitmentDuringLastYears();
+ final String[] riverBasinNames = rioBasinNetwork.getRiverBasinNames();
+
+ // TODO very risky since dependinf of basin order
+ for (int i = 0; i < riverBasinNames.length; i++) {
+ int presence = presences.get(period).get(riverBasinNames[i]);
+ if (presence == 0) {
+ sumLogWhereAbs += Math.log(1 - probOfNonNulRecruitmentDuringLastYears[i]);
+ } else {
+ sumLogWherePres += Math.log(probOfNonNulRecruitmentDuringLastYears[i]);
+ }
+ }
+
+ return sumLogWhereAbs + sumLogWherePres;
+ }
+
+
+ public double getNorthernmostPopulatedLatitude(DiadromousFishGroup group) {
+ double latitude = 0;
+
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ double meanLastRecruitment = riverBasin.getLastRecruitments().getMean();
+
+ if (meanLastRecruitment >= minimumRecruitsForPopulatedBasin) {
+ // the river basin is considered populated
+
+ // northern edge
+ if (riverBasin.getLatitude() > latitude) {
+ // the basin is the new northern edge
+ latitude = riverBasin.getLatitude();
+ }
+ }
+ }
+ return latitude;
+ }
+
+
+ public double computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(double TARGET, DiadromousFishGroup group) {
+ double sum = 0;
+ for (RiverBasin riverBasin : group.getEnvironment().getRiverBasins()) {
+ if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() > 0.) {
+ double val = riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() - TARGET;
+ sum += val * val;
+ }
+ }
+ // System.out.println("sum female: " + sum);
+ return sum;
+ }
+
+ public double computeFemaleSpawnerForFirstTimeSummaryStatistic(DiadromousFishGroup group) {
+ return computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(targetedAgeForFemaleSpawnerForFirstTime, group);
+ }
}
diff --git a/src/main/java/species/DiadromousFishGroup.java b/src/main/java/species/DiadromousFishGroup.java
index 78c25df5e1a5b9ccc3c0e55c1886401834b1c0ef..3169f364fc21fd64522fd4ad5f0bc9a749690529 100644
--- a/src/main/java/species/DiadromousFishGroup.java
+++ b/src/main/java/species/DiadromousFishGroup.java
@@ -14,8 +14,6 @@ import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Scanner;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import java.util.regex.Pattern;
import org.openide.util.lookup.ServiceProvider;
@@ -31,9 +29,7 @@ import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
import fr.cemagref.simaqualife.kernel.Processes;
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.Duo;
-import miscellaneous.TreeMapForCentile;
import species.DiadromousFish.Gender;
-import species.DiadromousFish.Stage;
/**
*
@@ -58,15 +54,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
*/
private NutrientRoutine nutrientRoutine;
- public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
-
- /**
- * centile to calcucale the range of species distribution
- *
- * @unit
- */
- public double centileForRange = 0.95;
-
/**
* file with the calibated parameters (from baysian approach)
*
@@ -179,23 +166,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
*/
private transient List<Duo<Double, Double>> parameterSets;
- // =================================================
- // calibration
- // =================================================
-
- @Deprecated
- private Double targetedAgeForFemaleSpawnerForFirstTime = 5.5;
- @Deprecated
- private Double targetedAgeForMaleSpawnerForFirstTime = 4.5;
-
- /**
- * map of observedoccurence in 1900
- *
- * @unit
- */
- @Deprecated
- private transient Map<String, Integer> obs1900;
-
public static void main(String[] args) {
DiadromousFishGroup diadromousFishGroup = new DiadromousFishGroup(new Pilot(), null, null);
@@ -479,44 +449,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
e.printStackTrace();
}
}
- // ------------------------------------------------------------------
- // read occurence data file
- // -----------------------------------------------------------
- FileReader reader;
- Scanner scanner;
-
- obs1900 = new HashMap<String, Integer>();
- if (!fileNameInputForInitialObservation.isEmpty()) {
- try {
- reader = new FileReader(fileNameInputForInitialObservation);
- // Parsing the file
- scanner = new Scanner(reader);
- scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
- scanner.useDelimiter(Pattern.compile("[;\r]"));
-
- scanner.nextLine(); // to skip the file first line of headers
-
- while (scanner.hasNextLine()) {
- String[] fields = scanner.nextLine().split(",");
- // System.out.println(Arrays.toString(fields));
- if (fields.length > 2) {
- if (!fields[2].isEmpty())
- obs1900.put(fields[1], Integer.valueOf(fields[2]));
- }
- }
-
- reader.close();
- scanner.close();
-
- } catch (IOException ex) {
- Logger.getLogger(DiadromousFishGroup.class.getName()).log(Level.SEVERE, null, ex);
- }
- }
- // defaut values
- if (targetedAgeForFemaleSpawnerForFirstTime == null)
- targetedAgeForFemaleSpawnerForFirstTime = 5.5;
- if (targetedAgeForMaleSpawnerForFirstTime == null)
- targetedAgeForMaleSpawnerForFirstTime = 4.5;
// this.nutrientRoutine.getNutrientFluxesCollection().setBasinNames(this.getEnvironment().getRiverBasinNames());
this.nutrientRoutine.createNutrienFluxesCollections(this.getEnvironment().getRiverBasinNames());
@@ -614,6 +546,7 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
}
+ @Deprecated
public double getStandardDeviationOfMatureFishLength() {
double standardDeviationOfMatureFishLength = 0.;
double sumOfSquareLength = 0.;
@@ -692,264 +625,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
}
- // ================================================================
- // statictis for calibration
- // ================================================================
- @Deprecated
- public double computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(double TARGET) {
- double sum = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() > 0.) {
- double val = riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() - TARGET;
- sum += val * val;
- }
- }
- // System.out.println("sum female: " + sum);
- return sum;
- }
-
-
- @Deprecated
- @Observable(description = "Female spawners For First Time Summary Statistic")
- public double computeFemaleSpawnerForFirstTimeSummaryStatistic() {
- return computeFemaleSpawnerForFirstTimeSummaryStatisticWithTarget(targetedAgeForFemaleSpawnerForFirstTime);
- }
-
-
- @Deprecated
- @Observable(description = "mean age at first reproduction for female")
- public double getMeanAgeOfFirstReprodutionForFemale() {
- double sum = 0;
- double nb = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero() > 0.) {
- nb++;
- sum += riverBasin.getSpawnersForFirstTimeMeanAges(Gender.FEMALE).getMeanWithoutZero();
- }
- }
- return sum / nb;
- }
-
-
- @Deprecated
- @Observable(description = "mean length of first reprodution for female")
- public double getMeanLengthOfFirstReprodutionForFemale() {
- double sum = 0;
- double nb = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.FEMALE).getMeanWithoutZero() > 0.) {
- nb++;
- sum += riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.FEMALE).getMeanWithoutZero();
- }
- }
- return sum / nb;
- }
-
-
- @Deprecated
- public double computeMaleSpawnerForFirstTimeSummaryStatisticWithTarget(double TARGET) {
- double sum = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero() > 0.) {
- double val = riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero() - TARGET;
- sum += val * val;
- }
- }
- // System.out.println("sum male: " + sum);
- return sum;
- }
-
-
- @Deprecated
- @Observable(description = "Male spawners For First Time Summary Statistic")
- public double computeMaleSpawnerForFirstTimeSummaryStatistic() {
- return computeMaleSpawnerForFirstTimeSummaryStatisticWithTarget(targetedAgeForFemaleSpawnerForFirstTime);
- }
-
-
- @Deprecated
- @Observable(description = "mean age of first reprodution for male")
- public double getMeanAgeOfFirstReprodutionForMale() {
- double sum = 0;
- double nb = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero() > 0.) {
- nb++;
- sum += riverBasin.getSpawnersForFirstTimeMeanAges(Gender.MALE).getMeanWithoutZero();
- }
- }
- return sum / nb;
- }
-
-
- @Observable(description = "mean length of first reprodution for male")
- public double getMeanLengthOfFirstReprodutionForMale() {
- double sum = 0;
- double nb = 0;
- for (RiverBasin riverBasin : getEnvironment().getRiverBasins()) {
- if (riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.MALE).getMeanWithoutZero() > 0.) {
- nb++;
- sum += riverBasin.getSpawnersForFirstTimeMeanLengths(Gender.MALE).getMeanWithoutZero();
- }
- }
- return sum / nb;
- }
-
-
- @Deprecated
- @Observable(description = "Likelihood Summary stat")
- public double computeLikelihood() {
- int obsVal;
- double sumLogWherePres = 0.;
- double sumLogWhereAbs = 0.;
- final double[] probOfNonNulRecruitmentDuringLastYears = getEnvironment().getProbOfNonNulRecruitmentDuringLastYears();
- final String[] finalStatesNames = getEnvironment().getRiverBasinNames();
- for (int i = 0; i < finalStatesNames.length; i++) {
- if (obs1900.containsKey(finalStatesNames[i])) {
- obsVal = obs1900.get(finalStatesNames[i]);
- if (obsVal == 0) {
- sumLogWhereAbs += Math.log(1 - probOfNonNulRecruitmentDuringLastYears[i]);
- } else {
- sumLogWherePres += Math.log(probOfNonNulRecruitmentDuringLastYears[i]);
- }
- }
- }
-
- return sumLogWhereAbs + sumLogWherePres;
- }
-
-
- // ========================================================
- // observer to explore fish distribution
- // ========================================================
- @Deprecated
- @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;
- }
-
-
- @Deprecated
- @Observable(description = "Number of colonized basins")
- public double getNbColonizedBasins() {
- int nb = 0;
- for (Basin seaBasin : getEnvironment().getSeaBasins()) {
- if (seaBasin.getFishs(this) != null) {
- if (!seaBasin.getFishs(this).isEmpty()) {
- nb++;
- }
- }
- }
- return nb;
- }
-
-
- @Deprecated
- @Observable(description = "Northern colonized basins")
- public double getNorthernBasins() {
- int northernBasin = Integer.MAX_VALUE;
- for (Basin seaBasin : getEnvironment().getSeaBasins()) {
- if (seaBasin.getFishs(this) != null) {
- if (!seaBasin.getFishs(this).isEmpty()) {
- northernBasin = Math.min(northernBasin, getEnvironment().getAssociatedRiverBasin(seaBasin).getId());
- }
- }
- }
- return northernBasin;
- }
-
-
- @Deprecated
- @Observable(description = "Southern colonized basins")
- public double getSouthernBasins() {
- int southernBasin = Integer.MIN_VALUE;
- for (Basin seaBasin : getEnvironment().getSeaBasins()) {
- if (seaBasin.getFishs(this) != null) {
- if (!seaBasin.getFishs(this).isEmpty()) {
- southernBasin = Math.max(southernBasin, getEnvironment().getAssociatedRiverBasin(seaBasin).getId());
- }
- }
- }
- return southernBasin;
- }
-
-
- @Deprecated
- @Observable(description = "Range distribution with latitude")
- public Double[] getRangeDistributionWithLat() {
- // TODO keep the extreme latitudes from the catchment
- double southernBasin = 35.;
- double northernBasin = 60.;
- RiverBasin riverBasin;
- TreeMapForCentile latitudeEffective = new TreeMapForCentile();
- for (Basin seaBasin : getEnvironment().getSeaBasins()) {
- if (seaBasin.getFishs(this) != null) {
- if (!seaBasin.getFishs(this).isEmpty()) {
- riverBasin = getEnvironment().getAssociatedRiverBasin(seaBasin);
- long effective = 0;
- for (DiadromousFish fish : seaBasin.getFishs(this)) {
- effective += fish.getAmount();
- }
- southernBasin = Math.max(southernBasin, riverBasin.getLatitude());
- latitudeEffective.putWithAdding(riverBasin.getLatitude(), effective);
- northernBasin = Math.min(northernBasin, riverBasin.getLatitude());
- }
- }
- }
-
- Double[] rangeDistribution = new Double[4];
-
- rangeDistribution[0] = (latitudeEffective.isEmpty() ? (southernBasin + northernBasin) / 2.
- : latitudeEffective.calculateMedian());
- rangeDistribution[1] = Math.min(southernBasin, northernBasin);
- rangeDistribution[2] = Math.max(southernBasin, northernBasin);
- rangeDistribution[3] = latitudeEffective.calculateCentile(centileForRange);
- return rangeDistribution;
- }
-
-
- @Deprecated
- @Observable(description = "Range distribution")
- public double[] getRangeDistribution() {
- double southernBasin = 0;
- double nbBasin = getEnvironment().getNbRiverBasin();
- double northernBasin = nbBasin;
- Basin riverBasin;
- TreeMapForCentile latitudeEffective = new TreeMapForCentile();
- for (Basin seaBasin : getEnvironment().getSeaBasins()) {
- if (seaBasin.getFishs(this) != null) {
- if (!seaBasin.getFishs(this).isEmpty()) {
- riverBasin = getEnvironment().getAssociatedRiverBasin(seaBasin);
- long effective = 0;
- for (DiadromousFish fish : seaBasin.getFishs(this)) {
- effective += fish.getAmount();
- }
- latitudeEffective.putWithAdding(riverBasin.getId(), effective);
- southernBasin = Math.max(southernBasin, riverBasin.getId());
- northernBasin = Math.min(northernBasin, riverBasin.getId());
- }
- }
- }
- southernBasin = nbBasin - southernBasin;
- northernBasin = nbBasin - northernBasin;
- double[] rangeDistribution = new double[3];
- rangeDistribution[0] = (latitudeEffective.isEmpty() ? (southernBasin + northernBasin) / 2.
- : nbBasin - latitudeEffective.calculateMedian());
- rangeDistribution[1] = Math.min(southernBasin, northernBasin);
- rangeDistribution[2] = Math.max(southernBasin, northernBasin);
-
- return rangeDistribution;
- }
-
-
// ========================================================
// observer to explore fish abundance
// ========================================================
@@ -970,63 +645,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
}
- /**
- * @return sum of spawner effectives in all the river basins
- */
- @Observable(description = "Number of spawners in river basins")
- @Deprecated
- public double getSpawnerEffective() {
- long eff = 0;
- for (RiverBasin basin : this.getEnvironment().getRiverBasins()) {
- if (basin.getFishs(this) != null) {
- for (DiadromousFish fish : basin.getFishs(this)) {
- if (fish.getStage() == Stage.MATURE)
- eff += fish.getAmount();
- }
- }
- }
- return eff;
- }
-
-
- /**
- * @return sum of male spawner effectives in all basins
- */
- @Observable(description = "Number of male spawners in all basins")
- @Deprecated
- public double getMaleSpawnerEffective() {
- long eff = 0;
- for (Basin basin : this.getEnvironment().getBasins()) {
- if (basin.getFishs(this) != null) {
- for (DiadromousFish fish : basin.getFishs(this)) {
- if (fish.getStage() == Stage.MATURE && fish.getGender() == Gender.MALE)
- eff += fish.getAmount();
- }
- }
- }
- return eff;
- }
-
-
- /**
- * @return sum of female spawner effectives in all basins
- */
- @Observable(description = "Number of female spawners in all basins")
- @Deprecated
- public double getFemaleSpawnerEffective() {
- long eff = 0;
- for (Basin basin : this.getEnvironment().getBasins()) {
- if (basin.getFishs(this) != null) {
- for (DiadromousFish fish : basin.getFishs(this)) {
- if (fish.getStage() == Stage.MATURE && fish.getGender() == Gender.FEMALE)
- eff += fish.getAmount();
- }
- }
- }
- return eff;
- }
-
-
@Override
public void addAquaNism(DiadromousFish fish) {
// avoid utilisation of global fishes list