List of usage examples for org.apache.commons.math3.stat.inference OneWayAnova anovaPValue
public double anovaPValue(final Collection<double[]> categoryData) throws NullArgumentException, DimensionMismatchException, ConvergenceException, MaxCountExceededException
double[] arrays. From source file:coolmap.utils.statistics.test.CTest.java
public static void anova(CoolMapObject obj, Dimension direction, VNode... nodes) { try {/*from ww w . ja va 2s. c o m*/ ArrayList<VNode> leafNodes = new ArrayList<VNode>(); if (direction == Dimension.ROW) { leafNodes.addAll(obj.getViewNodesRow()); } else if (direction == Dimension.COLUMN) { leafNodes.addAll(obj.getViewNodesColumn()); } else { return; } ArrayList<double[]> data = new ArrayList<double[]>(); if (direction == Dimension.ROW) { for (VNode node : nodes) { data.add(extractRow(obj, node)); } } else if (direction == Dimension.COLUMN) { for (VNode node : nodes) { data.add(extractColumn(obj, node)); } } OneWayAnova anova = new OneWayAnova(); double pValue = anova.anovaPValue(data); TestResult result = new TestResult("One-way ANOVA", "One way analysis of variance wiht alpha = 0.05. \nData: " + obj.getName() + "\nDirection: " + direction + "\nGroups: " + Arrays.toString(nodes), pValue); CMConsole.log(result.toString()); } catch (Exception e) { CMConsole.logError( "ANOVA error: " + " Dataset:" + obj + " Direction:" + direction + " Groups:" + nodes == null ? null : Arrays.toString(nodes)); } }
From source file:fNIRs.FNIRsStats.java
private static void runANOVATests() { System.out.println("Running ANOVA tests."); File groupFile = new File("c:/Users/nkolesar/Desktop/CS Seminar/fNIRs/sub19/ANOVA Testing/legitGroups"); File hbFile = new File("C:/Users/nkolesar/Desktop/CS Seminar/fNIRs/sub19/ANOVA Testing/legitHb"); int precision = 7; int numChunks = 10; GroupedChannels groups1 = new GroupedChannels(hbFile, groupFile); String groupName = "groupOne"; runANOVATestsHelper(groups1, groupName, 0); runANOVATestsHelper(groups1, groupName, 1); LinkedList<double[]> container = new LinkedList<double[]>(); container.add(toPrimitiveDoubleArray(groups1.getGroup(groupName).getData(0))); container.add(toPrimitiveDoubleArray(groups1.getGroup(groupName).getData(1))); OneWayAnova myANOVA = new OneWayAnova(); double result = -1; result = myANOVA.anovaPValue(container); System.out.println("Result: " + result); // outputANOVAs(groups1, // groups1.getGroupNames(), groups1.getConditions(), // numChunks, precision); File outFile = new File("C:/Users/nkolesar/Desktop/CS Seminar/fNIRs/sub19/ANOVA Testing/outputFile.csv"); writeANOVAs(outFile, groups1, groups1.getGroupNames(), groups1.getConditions(), // groupNames, conditions, numChunks, precision);/*from w w w . ja va2 s . c o m*/ System.out.println("Done."); }
From source file:fNIRs.FNIRsStats.java
public static void oldOutputANOVAs(GroupedChannels data, List<String> groupNames, List<Integer> conditions, int numChunks, int precision) { // get all condition-group sequences: ArrayList<GroupedChannels.TaggedDataSequence> allTDSs = data.getAllSelectedTDSs(groupNames, conditions); chunkData(allTDSs, numChunks); // COMMENT THIS LATER // calculate required widths for printed names and condition numbers: int nameWidth = longestLength(groupNames); // length of longest name int conditionWidth = // number of digits in the largest condition number String.valueOf(Collections.max(conditions)).length(); // make sure the fields will be wide enough to hold the ANOVA values, // which will, in the widest case, consist of a 1 followed by a . and // precision 0s: // AM I USING "PRECISION" RIGHT? int idFieldWidth = nameWidth + conditionWidth + 2; if (idFieldWidth < precision + 2) { // for the "1." // if not, increase the condition width so the total field width is // large enough: idFieldWidth = precision + 2;/*from www . j ava 2s . c o m*/ } String idFieldFormat = "%-" + idFieldWidth + "s"; // output the first row, containing identifying information for each // group-condition combination: // first, output proper-width placeholder for the identifier column: System.out.printf("%" + idFieldWidth + "s ", ""); // TOO HACKY?? // then, output all tds identifiers: for (GroupedChannels.TaggedDataSequence tds : allTDSs) { System.out.printf(idFieldFormat + " ", tds.getGroupName() + " c" + tds.getCondition()); } System.out.println(); // print newline // output ANOVA values line by line: OneWayAnova myANOVA = new OneWayAnova(); for (GroupedChannels.TaggedDataSequence first : allTDSs) { // output tds identifier in first column: System.out.printf(idFieldFormat + " ", first.getGroupName() + " c" + first.getCondition()); // create Collection to send to the ANOVA object: LinkedList<double[]> dataSets = new LinkedList<double[]>(); // convert first's data sequence to an array, then add it to // dataSets dataSets.add(toPrimitiveDoubleArray(first.getData())); dataSets.add(null); // placeholder for second's data sequence for (GroupedChannels.TaggedDataSequence second : allTDSs) { // convert and add second's data sequence to position one in // dataSets: dataSets.set(1, toPrimitiveDoubleArray(second.getData())); double result = -1; // not a valid ANOVA value so we know if // something went wrong try { result = myANOVA.anovaPValue(dataSets); } catch (Exception ex) { System.out.println(); localError("unknown problem calculating ANOVA: " + ex.getMessage()); } System.out.printf("%-" + idFieldWidth + "." + precision + "f ", result); // dataSets.remove(1); // remove second's data from dataSets } System.out.println(); // print newline } }
From source file:fNIRs.FNIRsStats.java
public static void oldWriteANOVAs(File outFile, GroupedChannels data, List<String> groupNames, List<Integer> conditions, int numChunks, int precision) { // open file for writing with a nice print stream object: PrintWriter ostream = makePWriter(outFile); // OKAY VAR NAME? // get all condition-group sequences: ArrayList<GroupedChannels.TaggedDataSequence> allTDSs = data.getAllSelectedTDSs(groupNames, conditions); // chunkData(allTDSs, numChunks); // COMMENT THIS LATER // calculate required widths for printed names and condition numbers: int nameWidth = longestLength(groupNames); // length of longest name int conditionWidth = // number of digits in the largest condition number String.valueOf(Collections.max(conditions)).length(); // make sure the fields will be wide enough to hold the ANOVA values, // which will consist of a 0 or 1 followed by a . and precision 0s: int idFieldWidth = nameWidth + 2 + conditionWidth; // 2 == " c".length() if (idFieldWidth < precision + 2) { // 2 == "1.".length() // if not, increase the condition width so the total field width is // large enough: // System.out.println("ANOVA values are wider than identifiers."); idFieldWidth = precision + 2;//from w ww .j a v a 2 s. c om } String idFieldFormat = "%-" + idFieldWidth + "s"; // format string // output the first row, containing identifying information for each // group-condition combination: // first, output proper-width placeholder for the identifier column: ostream.printf("%" + idFieldWidth + "s ", ""); // TOO HACKY?? // then, output all tds identifiers: for (GroupedChannels.TaggedDataSequence tds : allTDSs) { ostream.printf(idFieldFormat + " ", tds.getGroupName() + " c" + tds.getCondition()); // ostream.printf(idFieldFormat + " ", // tds.getGroupName(), // tds.getCondition()); } ostream.println(); // print newline // output ANOVA values line by line: OneWayAnova myANOVA = new OneWayAnova(); for (GroupedChannels.TaggedDataSequence first : allTDSs) { // output tds identifier in first column: ostream.printf(idFieldFormat + " ", first.getGroupName() + " c" + first.getCondition()); // create Collection to send to the ANOVA object: LinkedList<double[]> dataSets = new LinkedList<double[]>(); // convert first's data sequence to an array, then add it to // dataSets dataSets.add(toPrimitiveDoubleArray(first.getData())); dataSets.add(null); // placeholder for second's data sequence for (GroupedChannels.TaggedDataSequence second : allTDSs) { // convert and add second's data sequence to position one in // dataSets: dataSets.set(1, toPrimitiveDoubleArray(second.getData())); double result = -1; // not a valid ANOVA value so we know if // something went wrong try { result = myANOVA.anovaPValue(dataSets); // if (first == second) { // if the two TDSs are the same // TDS, // result = 1; // then the ANOVA value should be 1, even // though a divide-by-zero // } } catch (Exception ex) { ostream.println(); localError("unknown problem calculating ANOVA: " + ex.getMessage()); } if (result != result) { // if result is NaN System.out.println("NaN on " + first.getGroupName() + " c" + first.getCondition() + " and " + second.getGroupName() + " c" + second.getCondition()); } ostream.printf("%-" + idFieldWidth + "." + precision + "f ", result); } ostream.println(); // print newline } ostream.close(); }
From source file:fNIRs.FNIRsStats.java
public static void writeANOVAs(File outFile, GroupedChannels data, List<String> groupNames, List<Integer> conditions, int numChunks, int precision) { // open file for writing with a nice print stream object: PrintWriter ostream = makePWriter(outFile); // OKAY VAR NAME? // get all condition-group sequences: ArrayList<GroupedChannels.TaggedDataSequence> allTDSs = data.getAllSelectedTDSs(groupNames, conditions); // chunkData(allTDSs, numChunks); // COMMENT THIS LATER int idFieldWidth = getIdFieldWidth(groupNames, conditions, precision); String idFieldFormat = "%-" + idFieldWidth + "s"; // format string String separator = " , "; // what goes between columns of output // output the first row, containing identifying information for each // group-condition combination: // first, output spaces to take the place of the identifier column: ostream.printf("%" + idFieldWidth + "s" + separator, ""); // TOO HACKY?? // then, output all tds identifiers: for (GroupedChannels.TaggedDataSequence tds : allTDSs) { ostream.printf(idFieldFormat + separator, tds.getGroupName() + " c" + tds.getCondition()); }/*from w w w .j a v a 2s . c o m*/ ostream.println(); // print newline // output ANOVA values line by line: OneWayAnova myANOVA = new OneWayAnova(); // this object will do the // ANOVAs for (GroupedChannels.TaggedDataSequence first : allTDSs) { // output tds identifier in first column: ostream.printf(idFieldFormat + separator, first.getGroupName() + " c" + first.getCondition()); // create Collection to send to the ANOVA object: LinkedList<double[]> dataSets = new LinkedList<double[]>(); // convert first's data sequence to an array, then add it to // dataSets dataSets.add(toPrimitiveDoubleArray(first.getData())); dataSets.add(null); // placeholder for second's data sequence for (GroupedChannels.TaggedDataSequence second : allTDSs) { // convert and add second's data sequence to position one in // dataSets: dataSets.set(1, toPrimitiveDoubleArray(second.getData())); double result = -1; // not a valid ANOVA value so we know if // something went wrong try { result = myANOVA.anovaPValue(dataSets); // if (first == second) { // if the two TDSs are the same // TDS, // result = 1; // then the ANOVA value should be 1, even // though a divide-by-zero // } } catch (Exception ex) { ostream.println(); System.out.println("foo"); localError("unknown problem calculating ANOVA: " + ex.getMessage()); System.out.println( "---------------------------------------------------------------------------------------------------------------------------------------"); for (double[] set : dataSets) { printDoubleAry(set); System.out.println("---------------------------------------"); } } if (result != result) { // if result is NaN System.out.println("NaN on " + first.getGroupName() + " c" + first.getCondition() + " and " + second.getGroupName() + " c" + second.getCondition()); } // AGAIN, SEE IF "PRECISON" == "NUMBER OF DECIMAL PLACES" ostream.printf("%-" + idFieldWidth + "." + precision + "f" + separator, result); } ostream.println(); // print newline } ostream.close(); }
From source file:fNIRs.FNIRsStats.java
public static void outputANOVAs(GroupedChannels data, List<String> groupNames, List<Integer> conditions, int numChunks, int precision) { // get all condition-group sequences: ArrayList<GroupedChannels.TaggedDataSequence> allTDSs = data.getAllSelectedTDSs(groupNames, conditions); chunkData(allTDSs, numChunks); // COMMENT THIS LATER int idFieldWidth = getIdFieldWidth(groupNames, conditions, precision); // create a format string for the group/condition combination identifier // fields in the output: String idFieldFormat = "%-" + idFieldWidth + "s"; // format string String separator = " , "; // what goes between columns of output // output the first row, containing identifying information for each // group-condition combination: // first, output proper-width placeholder for the identifier column: System.out.printf("%" + idFieldWidth + "s" + separator, ""); // TOO // HACKY??//from w w w . j a va 2 s .c o m // then, output all tds identifiers: for (GroupedChannels.TaggedDataSequence tds : allTDSs) { System.out.printf(idFieldFormat + separator, tds.getGroupName() + " c" + tds.getCondition()); // System.out.printf(idFieldFormat + " ", // tds.getGroupName(), // tds.getCondition()); } System.out.println(); // print newline // output ANOVA values line by line: OneWayAnova myANOVA = new OneWayAnova(); for (GroupedChannels.TaggedDataSequence first : allTDSs) { // output tds identifier in first column: System.out.printf(idFieldFormat + separator, first.getGroupName() + " c" + first.getCondition()); // create Collection to send to the ANOVA object: LinkedList<double[]> dataSets = new LinkedList<double[]>(); // convert first's data sequence to an array, then add it to // dataSets dataSets.add(toPrimitiveDoubleArray(first.getData())); dataSets.add(null); // placeholder for second's data sequence for (GroupedChannels.TaggedDataSequence second : allTDSs) { // convert and add second's data sequence to position one in // dataSets: // dataSets.add(second.getData().toArray()); dataSets.set(1, toPrimitiveDoubleArray(second.getData())); double result = -1; // so it'll be obvious something's wrong // later if this doesn't get changed try { result = myANOVA.anovaPValue(dataSets); } catch (Exception ex) { System.out.println(); localError("unknown problem calculating ANOVA: " + ex.getMessage()); } System.out.printf("%-" + idFieldWidth + "." + precision + "f" + separator, result); // dataSets.remove(1); // remove second's data from dataSets } System.out.println(); // print newline } }
From source file:org.apache.solr.client.solrj.io.eval.AnovaEvaluator.java
@Override public Object doWork(Object... values) throws IOException { // at this point we know every incoming value is an array of BigDecimals List<double[]> anovaInput = Arrays.stream(values) // for each List, convert to double[] .map(value -> ((List<BigDecimal>) value).stream().mapToDouble(BigDecimal::doubleValue).toArray()) // turn into List<double[]> .collect(Collectors.toList()); OneWayAnova anova = new OneWayAnova(); double p = anova.anovaPValue(anovaInput); double f = anova.anovaFValue(anovaInput); Map<String, Number> m = new HashMap<>(); m.put("p-value", p); m.put("f-ratio", f); return new Tuple(m); }