public void doRFileEvaluate(final IScope scope, final IContainer param) {
int size = param.length(scope);
// if ( size == 0 ) { throw GamaRuntimeException.error("Missing Parameter Exception", scope); }
final String RFile = getPath();
try {
// Call R
RCaller caller = new RCaller();
String RPath = GamaPreferences.LIB_R.value(scope).getPath();
caller.setRscriptExecutable(RPath);
double[] vectorParam = new double[param.length(scope)];
int k = 0;
for (Object o : param.iterable(scope)) {
vectorParam[k++] = Cast.asFloat(scope, o);
}
RCode c = new RCode();
// Adding the parameters
c.addDoubleArray("vectorParam", vectorParam);
// Adding the codes in file
List<String> R_statements = new ArrayList<String>();
// tmthai.begin----------------------------------------------------------------------------
String fullPath = FileUtils.constructAbsoluteFilePath(scope, RFile, true);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.RScript:" + RPath);
GuiUtils.debug("Stats.R_compute_param.Param:" + vectorParam.toString());
GuiUtils.debug("Stats.R_compute_param.RFile:" + RFile);
GuiUtils.debug("Stats.R_compute_param.fullPath:" + fullPath);
}
// FileReader fr = new FileReader(RFile);
FileReader fr = new FileReader(fullPath);
// tmthai.end----------------------------------------------------------------------------
BufferedReader br = new BufferedReader(fr);
String statement;
while ((statement = br.readLine()) != null) {
c.addRCode(statement);
R_statements.add(statement);
// java.lang.System.out.println(statement);
}
br.close();
fr.close();
caller.setRCode(c);
GamaMap<String, IList> result = GamaMapFactory.create(Types.STRING, Types.LIST);
String var = computeVariable(R_statements.get(R_statements.size() - 1).toString());
caller.runAndReturnResult(var);
// DEBUG:
// java.lang.System.out.println("Name: '" + R_statements.length(scope) + "'");
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.R_statements.length: '" + R_statements.size() + "'");
}
for (String name : caller.getParser().getNames()) {
String[] results = null;
results = caller.getParser().getAsStringArray(name);
// java.lang.System.out.println("Name: '" + name + "'");
if (DEBUG) {
GuiUtils.debug(
"Stats.R_compute_param.caller.Name: '"
+ name
+ "' length: "
+ results.length
+ " - Value: "
+ results.toString());
}
result.put(name, GamaListFactory.create(scope, Types.NO_TYPE, results));
}
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.return:" + result.serialize(false));
}
setBuffer(result);
} catch (Exception ex) {
throw GamaRuntimeException.error("RCallerExecutionException " + ex.getMessage(), scope);
}
}
@operator(
value = {"percent_absolute_deviation"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {IConcept.STATISTIC})
@doc(
value =
"percent absolute deviation indicator for 2 series of values: percent_absolute_deviation(list_vals_observe,list_vals_sim)",
examples = {
@example(
value = "percent_absolute_deviation([200,300,150,150,200],[250,250,100,200,200])",
isExecutable = false)
})
public static double percentAbsoluteDeviation(
final IScope scope, final IList<Double> vals1, final IList<Double> vals2) {
if (vals1 == null || vals2 == null) {
return 1;
}
int nb = vals1.size();
if (nb != vals2.size()) {
return 0;
}
double sum = 0;
double coeff = 0;
for (int i = 0; i < nb; i++) {
double val1 = Cast.asFloat(scope, vals1.get(i));
double val2 = Cast.asFloat(scope, vals2.get(i));
coeff += val1;
sum += FastMath.abs(val1 - val2) * 100.0;
}
if (coeff == 0) {
return 0;
}
return sum / coeff;
}
@operator(
value = {"clustering_DBScan"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by DBScan Algorithm based on the given attributes. Some paremeters can be defined: "
+ "distance_f: The distance function to use for instances comparison (euclidean or manhattan); "
+ "min_points: minimun number of DataObjects required in an epsilon-range-query"
+ "epsilon: epsilon -- radius of the epsilon-range-queries",
examples = {
@example(
value =
"clustering_DBScan([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"distance_f\"::\"manhattan\"])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_simple_kmeans",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringDBScan(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
DBSCAN dbScan = new DBSCAN();
if (parameters != null) {
try {
if (parameters.containsKey("distance_f")) {
String distanceFct = Cast.asString(scope, parameters.get("distance_f"));
if (distanceFct.equals("manhattan")) {
dbScan.setDatabase_distanceType(ManhattanDataObject.class.getName());
} else {
dbScan.setDatabase_distanceType(EuclideanDistance.class.getName());
}
}
if (parameters.containsKey("min_points")) {
dbScan.setMinPoints(Cast.asInt(scope, parameters.get("min_points")));
}
if (parameters.containsKey("epsilon")) {
dbScan.setEpsilon(Cast.asInt(scope, parameters.get("epsilon")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, dbScan, attributes, agents);
return groupes;
}
@Override
public void firstLaunchOn(final IDisplaySurface surface) {
super.firstLaunchOn(surface);
final IExpression eventType = definition.getFacet(IKeyword.NAME);
final IExpression actionName = definition.getFacet(IKeyword.ACTION);
IScope scope = surface.getDisplayScope();
String currentMouseEvent = Cast.asString(scope, eventType.value(scope));
String currentAction = Cast.asString(scope, actionName.value(scope));
listener = new EventListener(surface, currentMouseEvent, currentAction);
surface.addMouseListener(listener);
}
@operator(
value = {"clustering_em"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by EM Algorithm based on the given attributes. Some paremeters can be defined: "
+ "max_iterations: the maximum number of iterations to perform;"
+ "num_clusters: the number of clusters; minStdDev: minimum allowable standard deviation",
examples = {
@example(
value =
"clustering_em([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"max_iterations\"::10, \"num_clusters\"::3])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_simple_kmeans",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringEM(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
EM em = new EM();
em.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("max_iterations")) {
em.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
}
if (parameters.containsKey("num_clusters")) {
em.setNumClusters(Cast.asInt(scope, parameters.get("num_clusters")));
}
if (parameters.containsKey("minStdDev")) {
em.setMinStdDev(Cast.asFloat(scope, parameters.get("minStdDev")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, em, attributes, agents);
return groupes;
}
@operator(
value = {"clustering_cobweb"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clusteredby CobWeb Algorithm based on the given attributes. Some paremeters can be defined: "
+ "acuity: minimum standard deviation for numeric attributes; "
+ "cutoff: category utility threshold by which to prune nodes seed",
examples = {
@example(
value =
"clustering_cobweb([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"acuity\"::3.0, \"cutoff\"::0.5)",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_simple_kmeans",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringCobweb(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
Cobweb cobweb = new Cobweb();
cobweb.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("acuity")) {
cobweb.setAcuity(Cast.asFloat(scope, parameters.get("acuity")));
}
if (parameters.containsKey("cutoff")) {
cobweb.setCutoff(Cast.asFloat(scope, parameters.get("cutoff")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, cobweb, attributes, agents);
return groupes;
}
private static Instances convertToInstances(
final IScope scope,
final IList<String> attributes,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents)
throws GamaRuntimeException {
FastVector attribs = new FastVector();
for (String att : attributes) {
attribs.addElement(new Attribute(att));
}
Instances dataset =
new Instances(scope.getAgentScope().getName(), attribs, agents.length(scope));
for (IAgent ag : agents.iterable(scope)) {
int nb = attributes.size();
double vals[] = new double[nb];
for (int i = 0; i < nb; i++) {
String attrib = attributes.get(i);
Double var = Cast.asFloat(scope, ag.getDirectVarValue(scope, attrib));
vals[i] = var;
}
Instance instance = new Instance(1, vals);
dataset.add(instance);
}
return dataset;
}
private static double computePo(
final IScope scope,
final IAgentFilter filter,
final Map<Object, Integer> categoriesId,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final int nbCat,
final int nb,
final IList<Double> similarities,
final IList<Object> weights) {
Map<IAgent, Integer> agsId = new TOrderedHashMap<IAgent, Integer>();
for (int i = 0; i < agents.length(scope); i++) {
agsId.put(agents.get(scope, i), i);
}
for (int i = 0; i < nb; i++) {
Object valObs = valsObs.get(i);
Object valSim = valsSim.get(i);
Object valInit = valsInit.get(i);
int valObsId = categoriesId.get(valObs);
int valSimId = categoriesId.get(valSim);
int valInitId = categoriesId.get(valInit);
IAgent agent = agents.get(scope, i);
double[] XaXs =
computeXaXs(
scope,
filter,
categoriesId,
agsId,
valObsId,
valSimId,
valInitId,
fuzzytransitions,
distance,
agent,
valsInit,
valsObs,
valsSim,
agents,
nbCat);
similarities.add(FastMath.min(XaXs[0], XaXs[1]));
}
double meanSimilarity = 0;
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
double val = weight * similarities.get(i);
total += weight;
meanSimilarity += val;
}
meanSimilarity /= total;
return meanSimilarity;
}
private static void computeXYCrispVector(
final IScope scope,
final Map<Object, Integer> categoriesId,
final List<Object> categories,
final IList<Object> vals1,
final IList<Object> vals2,
final GamaMatrix<Double> fuzzycategories,
final int nbCat,
final int nb,
final double[][] crispVector1,
final double[][] crispVector2,
final double[] X,
final double[] Y,
final boolean[] sim,
final IList<Object> weights) {
for (int j = 0; j < nbCat; j++) {
X[j] = 0;
Y[j] = 0;
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = vals1.get(i);
Object val2 = vals2.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
X[indexVal1] += weight;
Y[indexVal2] += weight;
for (int j = 0; j < nbCat; j++) {
crispVector1[i][j] = Cast.asFloat(scope, fuzzycategories.get(scope, indexVal1, j));
crispVector2[i][j] = Cast.asFloat(scope, fuzzycategories.get(scope, indexVal2, j));
}
if (val1.equals(val2)) {
sim[i] = true;
} else {
sim[i] = false;
}
}
for (int j = 0; j < nbCat; j++) {
X[j] /= total;
Y[j] /= total;
}
}
public FsmStateStatement(final IDescription desc) {
super(desc);
setName(getLiteral(IKeyword.NAME)); // A VOIR
isInitial = Cast.asBool(null, getLiteral(FsmStateStatement.INITIAL));
isFinal = Cast.asBool(null, getLiteral(FsmStateStatement.FINAL));
}
@operator(
value = {"kappa"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {})
@doc(
value =
"kappa indicator for 2 map comparisons: kappa(list_vals1,list_vals2,categories, weights). Reference: Cohen, J. A coefficient of agreement for nominal scales. Educ. Psychol. Meas. 1960, 20. ",
examples = {
@example(
value =
"kappa([cat1,cat1,cat2,cat3,cat2],[cat2,cat1,cat2,cat1,cat2],[cat1,cat2,cat3], [1.0, 2.0, 3.0, 1.0, 5.0])",
isExecutable = false)
})
public static double kappa(
final IScope scope,
final IList<Object> vals1,
final IList<Object> vals2,
final List<Object> categories,
final IList<Object> weights) {
if (vals1 == null || vals2 == null) {
return 1;
}
int nb = vals1.size();
if (nb != vals2.size()) {
return 0;
}
int nbCat = categories.size();
double[] X = new double[nbCat];
double[] Y = new double[nbCat];
double[][] contigency = new double[nbCat][nbCat];
for (int j = 0; j < nbCat; j++) {
X[j] = 0;
Y[j] = 0;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] = 0;
}
}
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = vals1.get(i);
Object val2 = vals2.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
X[indexVal1] += weight;
Y[indexVal2] += weight;
contigency[indexVal1][indexVal2] += weight;
}
for (int j = 0; j < nbCat; j++) {
X[j] /= total;
Y[j] /= total;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] /= total;
}
}
double po = 0;
double pe = 0;
for (int i = 0; i < nbCat; i++) {
po += contigency[i][i];
pe += X[i] * Y[i];
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
private static double computeSimilarity(
final IScope scope,
final IAgentFilter filter,
final Double distance,
final IList<Object> vals1,
final IList<Object> vals2,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final int nbCat,
final int nb,
final double[][] crispVector1,
final double[][] crispVector2,
final boolean[] sim,
final double[][] fuzzyVector1,
final double[][] fuzzyVector2,
final IList<Double> similarities,
final IList<Object> weights) {
Map<IAgent, Integer> agsId = new TOrderedHashMap<IAgent, Integer>();
for (int i = 0; i < agents.length(scope); i++) {
agsId.put(agents.get(scope, i), i);
}
for (int i = 0; i < nb; i++) {
if (sim[i]) {
similarities.add(1.0);
} else {
IAgent agent = agents.get(scope, i);
// double sizeNorm = agent.getPerimeter() / 4.0;
double sizeNorm = FastMath.sqrt(agent.getEnvelope().getArea());
List<IAgent> neighbors =
distance == 0 || filter == null
? new ArrayList<IAgent>()
: new ArrayList<IAgent>(
scope.getTopology().getNeighborsOf(scope, agent, distance, filter));
Map<IAgent, Double> distancesCoeff = new TOrderedHashMap<IAgent, Double>();
distancesCoeff.put(agent, 1.0);
for (IAgent ag : neighbors) {
double euclidDist = agent.getLocation().euclidianDistanceTo(ag.getLocation());
distancesCoeff.put(ag, 1 / (1.0 + euclidDist / sizeNorm));
}
for (int j = 0; j < nbCat; j++) {
double max1 = 0.0;
double max2 = 0.0;
for (IAgent ag : neighbors) {
int id = agsId.get(ag);
double val1 = crispVector1[id][j] * distancesCoeff.get(ag);
double val2 = crispVector2[id][j] * distancesCoeff.get(ag);
if (val1 > max1) {
max1 = val1;
}
if (val2 > max2) {
max2 = val2;
}
}
fuzzyVector1[i][j] = max1;
fuzzyVector2[i][j] = max2;
}
double s1Max = -1 * Double.MAX_VALUE;
double s2Max = -1 * Double.MAX_VALUE;
for (int j = 0; j < nbCat; j++) {
double s1 = FastMath.min(fuzzyVector1[i][j], crispVector2[i][j]);
double s2 = FastMath.min(fuzzyVector2[i][j], crispVector1[i][j]);
if (s1 > s1Max) {
s1Max = s1;
}
if (s2 > s2Max) {
s2Max = s2;
}
}
similarities.add(FastMath.min(s1Max, s2Max));
}
}
double meanSimilarity = 0;
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
double val = weight * similarities.get(i);
total += weight;
meanSimilarity += val;
}
meanSimilarity /= total;
return meanSimilarity;
}
@operator(
value = {"clustering_simple_kmeans"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by K-Means Algorithm based on the given attributes. Some paremeters can be defined: "
+ "distance_f: The distance function to use. 4 possible distance functions: euclidean (by default) ; 'chebyshev', 'manhattan' or 'levenshtein'; "
+ "dont_replace_missing_values: if false, replace missing values globally with mean/mode; max_iterations: the maximum number of iterations to perform;"
+ "num_clusters: the number of clusters",
examples = {
@example(
value =
"clustering_simple_kmeans([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"distance_f\"::\"manhattan\", \"num_clusters\"::3])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringSimpleKMeans(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
SimpleKMeans kmeans = new SimpleKMeans();
kmeans.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("distance_f")) {
String distanceFct = Cast.asString(scope, parameters.get("distance_f"));
if (distanceFct.equals("chebyshev")) {
kmeans.setDistanceFunction(new ChebyshevDistance());
} else if (distanceFct.equals("manhattan")) {
kmeans.setDistanceFunction(new ManhattanDistance());
} else if (distanceFct.equals("levenshtein")) {
kmeans.setDistanceFunction(new EditDistance());
}
}
if (parameters.containsKey("dont_replace_missing_values")) {
kmeans.setDontReplaceMissingValues(
Cast.asBool(scope, parameters.get("dont_replace_missing_values")));
}
if (parameters.containsKey("max_iterations")) {
kmeans.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
}
if (parameters.containsKey("num_clusters")) {
kmeans.setNumClusters(Cast.asInt(scope, parameters.get("num_clusters")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, kmeans, attributes, agents);
return groupes;
}
@operator(
value = {"fuzzy_kappa_sim"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {IConcept.MAP})
@doc(
value =
"fuzzy kappa simulation indicator for 2 map comparisons: fuzzy_kappa_sim(agents_list,list_vals1,list_vals2, output_similarity_per_agents,fuzzy_transitions_matrix, fuzzy_distance, weights). Reference: Jasper van Vliet, Alex Hagen-Zanker, Jelle Hurkens, Hedwig van Delden, A fuzzy set approach to assess the predictive accuracy of land use simulations, Ecological Modelling, 24 July 2013, Pages 32-42, ISSN 0304-3800, ",
examples = {
@example(
value =
"fuzzy_kappa_sim([ag1, ag2, ag3, ag4, ag5], [cat1,cat1,cat2,cat3,cat2],[cat2,cat1,cat2,cat1,cat2], similarity_per_agents,[cat1,cat2,cat3],[[1,0,0,0,0,0,0,0,0],[0,1,0,0,0,0,0,0,0],[0,0,1,0,0,0,0,0,0],[0,0,0,1,0,0,0,0,0],[0,0,0,0,1,0,0,0,0],[0,0,0,0,0,1,0,0,0],[0,0,0,0,0,0,1,0,0],[0,0,0,0,0,0,0,1,0],[0,0,0,0,0,0,0,0,1]], 2,[1.0,3.0,2.0,2.0,4.0])",
isExecutable = false)
})
public static double fuzzyKappaSimulation(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final IList<Double> similarities,
final List<Object> categories,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IList<Object> weights) {
if (agents == null) {
return 1;
}
int nb = agents.length(scope);
if (nb < 1) {
return 1;
}
similarities.clear();
int nbCat = categories.size();
double[] nbObs = new double[nbCat];
double[] nbSim = new double[nbCat];
double[] nbInit = new double[nbCat];
double[][] nbInitObs = new double[nbCat][nbCat];
double[][] nbInitSim = new double[nbCat][nbCat];
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
Map<List<Integer>, Map<Double, Double>> XaPerTransition =
new TOrderedHashMap<List<Integer>, Map<Double, Double>>();
Map<List<Integer>, Map<Double, Double>> XsPerTransition =
new TOrderedHashMap<List<Integer>, Map<Double, Double>>();
Set<Double> Xvals = new HashSet<Double>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
for (int i = 0; i < nbCat; i++) {
nbInit[i] = 0;
nbObs[i] = 0;
nbSim[i] = 0;
for (int j = 0; j < nbCat; j++) {
nbInitObs[i][j] = 0;
nbInitSim[i][j] = 0;
}
}
IAgentFilter filter = In.list(scope, agents);
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
int idCatInit = categoriesId.get(valsInit.get(i));
int idCatObs = categoriesId.get(valsObs.get(i));
int idCatSim = categoriesId.get(valsSim.get(i));
nbInit[idCatInit] += weight;
nbSim[idCatSim] += weight;
nbObs[idCatObs] += weight;
nbInitObs[idCatInit][idCatObs] += weight;
nbInitSim[idCatInit][idCatSim] += weight;
}
double po =
computePo(
scope,
filter,
categoriesId,
fuzzytransitions,
distance,
valsInit,
valsObs,
valsSim,
agents,
nbCat,
nb,
similarities,
weights);
double pe = 0;
computeXaXsTransitions(
scope,
filter,
fuzzytransitions,
distance,
agents,
nbCat,
XaPerTransition,
XsPerTransition,
Xvals);
for (int i = 0; i < nbCat; i++) {
for (int j = 0; j < nbCat; j++) {
for (int k = 0; k < nbCat; k++) {
List<Integer> ca = new ArrayList<Integer>();
ca.add(i);
ca.add(j);
ca.add(k);
Map<Double, Double> pmuXa = XaPerTransition.get(ca);
Map<Double, Double> pmuXs = XsPerTransition.get(ca);
double emu = 0;
for (Double xval : Xvals) {
double XaVal = pmuXa == null || !pmuXa.containsKey(xval) ? 0 : pmuXa.get(xval);
double XsVal = pmuXs == null || !pmuXs.containsKey(xval) ? 0 : pmuXs.get(xval);
double proba = xval * XaVal * XsVal;
emu += proba;
}
double poas = nbInit[i] == 0 ? 0 : nbInitObs[i][j] / nbInit[i] * nbInitSim[i][k] / total;
pe += emu * poas;
}
}
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
@operator(
value = {"kappa_sim"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {})
@doc(
value =
"kappa simulation indicator for 2 map comparisons: kappa(list_valsInits,list_valsObs,list_valsSim, categories, weights). Reference: van Vliet, J., Bregt, A.K. & Hagen-Zanker, A. (2011). Revisiting Kappa to account for change in the accuracy assessment of land-use change models, Ecological Modelling 222(8)",
examples = {
@example(
value =
"kappa([cat1,cat1,cat2,cat2,cat2],[cat2,cat1,cat2,cat1,cat3],[cat2,cat1,cat2,cat3,cat3], [cat1,cat2,cat3],[1.0, 2.0, 3.0, 1.0, 5.0])",
isExecutable = false)
})
public static double kappaSimulation(
final IScope scope,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final List<Object> categories,
final IList<Object> weights) {
if (valsInit == null || valsObs == null || valsSim == null) {
return 1;
}
int nb = valsInit.size();
if (nb != valsObs.size() || nb != valsSim.size()) {
return 0;
}
int nbCat = categories.size();
double[] O = new double[nbCat];
double[][] contigency = new double[nbCat][nbCat];
double[][] contigencyOA = new double[nbCat][nbCat];
double[][] contigencyOS = new double[nbCat][nbCat];
for (int j = 0; j < nbCat; j++) {
O[j] = 0;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] = 0;
contigencyOA[j][k] = 0;
contigencyOS[j][k] = 0;
}
}
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = valsObs.get(i);
Object val2 = valsSim.get(i);
Object valO = valsInit.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
int indexValO = categoriesId.get(valO);
O[indexValO] += weight;
contigency[indexVal1][indexVal2] += weight;
contigencyOA[indexValO][indexVal1] += weight;
contigencyOS[indexValO][indexVal2] += weight;
}
for (int j = 0; j < nbCat; j++) {
for (int k = 0; k < nbCat; k++) {
contigency[j][k] /= total;
if (O[j] > 0) {
contigencyOA[j][k] /= O[j];
contigencyOS[j][k] /= O[j];
}
}
O[j] /= total;
}
double po = 0;
double pe = 0;
for (int j = 0; j < nbCat; j++) {
po += contigency[j][j];
double sum = 0;
for (int i = 0; i < nbCat; i++) {
sum += contigencyOA[j][i] * contigencyOS[j][i];
}
pe += O[j] * sum;
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
@operator(
value = {"clustering_xmeans"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by X-Means Algorithm based on the given attributes. Some paremeters can be defined: bin_value: value given for true value of boolean attributes; cut_off_factor: the cut-off factor to use;"
+ "distance_f: The distance function to use. 4 possible distance functions: euclidean (by default) ; 'chebyshev', 'manhattan' or 'levenshtein'; "
+ "max_iterations: the maximum number of iterations to perform; max_kmeans: the maximum number of iterations to perform in KMeans; max_kmeans_for_children: the maximum number of iterations KMeans that is performed on the child centers;"
+ "max_num_clusters: the maximum number of clusters; min_num_clusters: the minimal number of clusters",
examples = {
@example(
value =
"clustering_xmeans([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\", \"is_male\"],[\"bin_value\"::1.0, \"distance_f\"::\"manhattan\", \"max_num_clusters\"::10, \"min_num_clusters\"::2])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_simple_kmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringXMeans(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters)
throws GamaRuntimeException {
XMeans xmeans = new XMeans();
xmeans.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
if (parameters.containsKey("bin_value")) {
xmeans.setBinValue(Cast.asFloat(scope, parameters.get("bin_value")));
}
if (parameters.containsKey("cut_off_factor")) {
xmeans.setCutOffFactor(Cast.asFloat(scope, parameters.get("cut_off_factor")));
}
if (parameters.containsKey("distance_f")) {
String distanceFct = Cast.asString(scope, parameters.get("distance_f"));
if (distanceFct.equals("chebyshev")) {
xmeans.setDistanceF(new ChebyshevDistance());
} else if (distanceFct.equals("manhattan")) {
xmeans.setDistanceF(new ManhattanDistance());
} else if (distanceFct.equals("levenshtein")) {
xmeans.setDistanceF(new EditDistance());
}
}
if (parameters.containsKey("max_iterations")) {
try {
xmeans.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
} catch (Exception e) {
}
}
if (parameters.containsKey("max_kmeans")) {
xmeans.setMaxKMeans(Cast.asInt(scope, parameters.get("max_kmeans")));
}
if (parameters.containsKey("max_kmeans_for_children")) {
xmeans.setMaxKMeansForChildren(
Cast.asInt(scope, parameters.get("max_kmeans_for_children")));
}
if (parameters.containsKey("max_num_clusters")) {
xmeans.setMaxNumClusters(Cast.asInt(scope, parameters.get("max_num_clusters")));
}
if (parameters.containsKey("min_num_clusters")) {
xmeans.setMinNumClusters(Cast.asInt(scope, parameters.get("min_num_clusters")));
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, xmeans, attributes, agents);
return groupes;
}
@Override
protected Object privateExecuteIn(final IScope scope) throws GamaRuntimeException {
// IGraph data = createData(scope);
IGraph g = Cast.asGraph(scope, getFacetValue(scope, IKeyword.GRAPH));
int thread_number =
Cast.asInt(
scope,
getFacetValue(
scope, GraphForceAtlasLayoutStatement.THREAD_NUMBER, THREAD_NUMBER_DEFAULT));
boolean dissuade_hubs =
Cast.asBool(
scope,
getFacetValue(
scope, GraphForceAtlasLayoutStatement.DISSUADE_HUBS, DISSUADE_HUBS_DEFAULT));
boolean linlog_mode =
Cast.asBool(
scope,
getFacetValue(scope, GraphForceAtlasLayoutStatement.LINLOG_MODE, LINLOG_MODE_DEFAULT));
boolean prevent_overlap =
Cast.asBool(
scope,
getFacetValue(
scope, GraphForceAtlasLayoutStatement.PREVENT_OVERLAP, PREVENT_OVERLAP_DEFAULT));
double edge_weight_influence =
Cast.asFloat(
scope,
getFacetValue(
scope,
GraphForceAtlasLayoutStatement.EDGE_WEIGHT_INFLUENCE,
EDGE_WEIGHT_INFLUENCE_DEFAULT));
double scaling =
Cast.asFloat(
scope, getFacetValue(scope, GraphForceAtlasLayoutStatement.SCALING, SCALING_DEFAULT));
boolean stronger_gravity =
Cast.asBool(
scope,
getFacetValue(
scope, GraphForceAtlasLayoutStatement.STRONGER_GRAVITY, STRONGER_GRAVITY_DEFAULT));
double gravity =
Cast.asFloat(
scope, getFacetValue(scope, GraphForceAtlasLayoutStatement.GRAVITY, GRAVITY_DEFAULT));
double tolerance =
Cast.asFloat(
scope,
getFacetValue(scope, GraphForceAtlasLayoutStatement.TOLERANCE, TOLERANCE_DEFAULT));
boolean approximate_repulsion =
Cast.asBool(
scope,
getFacetValue(
scope,
GraphForceAtlasLayoutStatement.APPROXIMATE_REPULSION,
APPROXIMATE_REPULSION_DEFAULT));
double approximation =
Cast.asFloat(
scope,
getFacetValue(
scope, GraphForceAtlasLayoutStatement.APPROXIMATION, APPROXIMATION_DEFAULT));
int nb_steps =
Cast.asInt(
scope, getFacetValue(scope, GraphForceAtlasLayoutStatement.NB_STEPS, NB_STEPS_DEFAULT));
Object bp1 = getFacetValue(scope, GraphForceAtlasLayoutStatement.BOUNDED_P1, null);
Object bp2 = getFacetValue(scope, GraphForceAtlasLayoutStatement.BOUNDED_P2, null);
// public static IGraph YifanHuLayout_Step_Unlimited(final IGraph g, double optimal_distance,
// double initial_step, double step_ratio, double convergence_threshold, double
// barnes_hut_theta) {
initializing();
// System.out.println("ForceAtlas2 algorithm (by step), starting.");
// System.out.println("converting ...");
IGraph_to_GraphModel(g);
// System.out.println("initializing ...");
ForceAtlas2 fa2Layout = new ForceAtlas2(new ForceAtlas2Builder());
initializing_GraphModel(g);
fa2Layout.resetPropertiesValues();
fa2Layout.setGraphModel(graph_model);
fa2Layout.setOutboundAttractionDistribution(dissuade_hubs);
fa2Layout.setLinLogMode(linlog_mode);
fa2Layout.setAdjustSizes(prevent_overlap);
fa2Layout.setEdgeWeightInfluence(edge_weight_influence);
fa2Layout.setScalingRatio(scaling);
fa2Layout.setStrongGravityMode(stronger_gravity);
fa2Layout.setGravity(gravity);
fa2Layout.setJitterTolerance(tolerance);
fa2Layout.setBarnesHutOptimize(approximate_repulsion);
fa2Layout.setBarnesHutTheta(approximation);
// System.out.println("working ...");
fa2Layout.initAlgo();
// System.out.println("working ...");
// int nbsteps=1;
// for (int i = 0; i < nbsteps && fa2Layout.canAlgo(); i++){
for (int i = 0; i < nb_steps; i++) {
fa2Layout.goAlgo();
}
fa2Layout.endAlgo();
// fa2Layout.goAlgo();
// fa2Layout.endAlgo();
if (bp1 != null && bp2 != null) {
ILocation p1 = Cast.asPoint(scope, bp1);
ILocation p2 = Cast.asPoint(scope, bp2);
Update_locations(
g,
FastMath.min(p1.getX(), p2.getX()),
FastMath.min(p1.getY(), p2.getY()),
FastMath.max(p1.getX(), p2.getX()),
FastMath.max(p1.getY(), p2.getY()));
} else {
Update_locations(g);
}
// System.out.println("ended.");
return g;
}
public void updateXValues(IScope scope, int chartCycle, int targetNb) {
Object xval, xlab;
if (this.useXSource || this.useXLabels) {
if (this.useXSource) {
xval = xsource.resolveAgainst(scope).value(scope);
} else {
xval = xlabels.resolveAgainst(scope).value(scope);
}
if (this.useXLabels) {
xlab = xlabels.resolveAgainst(scope).value(scope);
} else {
xlab = xsource.resolveAgainst(scope).value(scope);
}
if (xval instanceof GamaList) {
IList xv2 = Cast.asList(scope, xval);
IList xl2 = Cast.asList(scope, xlab);
if (this.useXSource && xv2.size() > 0 && xv2.get(0) instanceof Number) {
XSeriesValues = new ArrayList<Double>();
Xcategories = new ArrayList<String>();
for (int i = 0; i < xv2.size(); i++) {
XSeriesValues.add(new Double(Cast.asFloat(scope, xv2.get(i))));
Xcategories.add(Cast.asString(scope, xl2.get(i)));
}
} else {
if (xv2.size() > Xcategories.size()) {
Xcategories = new ArrayList<String>();
for (int i = 0; i < xv2.size(); i++) {
if (i >= XSeriesValues.size()) {
XSeriesValues.add(new Double(getXCycleOrPlusOneForBatch(scope, chartCycle)));
}
Xcategories.add(Cast.asString(scope, xl2.get(i)));
}
}
}
if (xv2.size() < targetNb) {
throw GamaRuntimeException.error(
"The x-serie length ("
+ xv2.size()
+ ") should NOT be shorter than any series length ("
+ targetNb
+ ") !",
scope);
}
} else {
if (this.useXSource && xval instanceof Number) {
double dvalue = Cast.asFloat(scope, xval);
String lvalue = Cast.asString(scope, xlab);
XSeriesValues.add(new Double(dvalue));
Xcategories.add(lvalue);
}
if (targetNb == -1 && !this.forceNoXAccumulate) targetNb = XSeriesValues.size() + 1;
while (XSeriesValues.size() < targetNb) {
XSeriesValues.add(new Double(getXCycleOrPlusOneForBatch(scope, chartCycle)));
Xcategories.add(Cast.asString(scope, xlab));
}
}
}
if (!this.useXSource && !this.useXLabels) {
if (targetNb == -1 && !this.forceNoXAccumulate && commonXindex >= XSeriesValues.size())
targetNb = XSeriesValues.size() + 1;
while (XSeriesValues.size() < targetNb) {
addCommonXValue(scope, getXCycleOrPlusOneForBatch(scope, chartCycle));
}
}
}
public static GamaColor staticCast(
final IScope scope, final Object obj, final Object param, final boolean copy)
throws GamaRuntimeException {
// param can contain the alpha value
if (obj instanceof GamaColor) {
GamaColor col = (GamaColor) obj;
if (param instanceof Integer) {
return new GamaColor(col.getRed(), col.getGreen(), col.getBlue(), (Integer) param);
} else if (param instanceof Double) {
return new GamaColor(col.getRed(), col.getGreen(), col.getBlue(), (Double) param);
} else {
return (GamaColor) obj;
}
}
if (obj instanceof List) {
List l = (List) obj;
int size = l.size();
if (size == 0) {
return new GamaColor(Color.black);
}
if (size == 1 || size == 2) {
return staticCast(scope, ((List) obj).get(0), param, copy);
} else if (size == 3) {
return new GamaColor(
Cast.asInt(scope, l.get(0)),
Cast.asInt(scope, l.get(1)),
Cast.asInt(scope, l.get(2)),
255);
} else if (size >= 4) {
return new GamaColor(
Cast.asInt(scope, l.get(0)),
Cast.asInt(scope, l.get(1)),
Cast.asInt(scope, l.get(2)),
Cast.asInt(scope, l.get(3)));
}
/* To allow constructions like rgb [255,255,255] */
}
if (obj instanceof IContainer) {
return staticCast(
scope, ((IContainer) obj).listValue(scope, Types.NO_TYPE, false), param, copy);
}
if (obj instanceof String) {
String s = ((String) obj).toLowerCase();
GamaColor c = GamaColor.colors.get(s);
if (c == null) {
try {
c = new GamaColor(Color.decode(s));
} catch (NumberFormatException e) {
GamaRuntimeException ex =
GamaRuntimeException.error("'" + s + "' is not a valid color name", scope);
throw ex;
}
GamaColor.colors.put(s, c);
}
if (param == null) {
return c;
} else if (param instanceof Integer) {
return new GamaColor(c, (Integer) param);
} else if (param instanceof Double) {
return new GamaColor(c, (Double) param);
}
}
if (obj instanceof Boolean) {
return (Boolean) obj ? new GamaColor(Color.black) : new GamaColor(Color.white);
}
int i = Cast.asInt(scope, obj);
GamaColor gc = GamaColor.getInt((255 & 0xFF) << 24 | i & 0xFFFFFF << 0);
if (param instanceof Integer) {
return new GamaColor(gc, (Integer) param);
} else if (param instanceof Double) {
return new GamaColor(gc, (Double) param);
}
return gc;
}