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Letting phase transition time points start later and end sooner for m…
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…ore comparable networks
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leifeld committed Feb 13, 2024
1 parent 91eb884 commit 6175742
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Showing 3 changed files with 68 additions and 41 deletions.
2 changes: 1 addition & 1 deletion build/bibliography.md
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Expand Up @@ -4,7 +4,7 @@ author:
bibliography:
- bibliography.bib
csl: apa-numeric-superscript-brackets.csl
date: 2024-02-10
date: 2024-02-13
title: "Discourse Network Analysis: Bibliography"
---

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2 changes: 1 addition & 1 deletion dna/src/main/java/dna/Dna.java
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Expand Up @@ -17,7 +17,7 @@ public class Dna {
public static Dna dna;
public static Logger logger;
public static Sql sql;
public static final String date = "2024-02-10";
public static final String date = "2024-02-13";
public static final String version = "3.0.11";
public static final String operatingSystem = System.getProperty("os.name");
public static File workingDirectory = null;
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105 changes: 66 additions & 39 deletions dna/src/main/java/export/Exporter.java
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Expand Up @@ -33,7 +33,6 @@
import java.time.format.DateTimeFormatter;
import java.time.temporal.WeekFields;
import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ThreadLocalRandom;
import java.util.stream.Collectors;
import java.util.stream.DoubleStream;
Expand Down Expand Up @@ -110,12 +109,28 @@ public class Exporter {
private SimulatedAnnealingBackboneResult simulatedAnnealingBackboneResult = null;

// time smoothing
/**
* Kernel function used for time slice network smoothing. Can be {@code "no"} (for no kernel function; uses legacy
* code instead); {@code "uniform"} (for uniform kernel, which is similar to "no"); {@code "epanechnikov"} (for the
* Epanechnikov kernel function; @code "triangular"} (for the triangular kernel function); or {@code "gaussian"}
* (for the Gaussian, or standard normal, kernel function).
*/
private String kernel = "no";
/**
* For kernel-smoothed time slices, should the first mid-point be half a bandwidth or time window duration after the
* start date and the last mid-point be half a bandwidth or duration before the last date to allow sufficient data
* around the end points of the timeline?
*/
private boolean indentBandwidth = true;

public void setKernelFunction(String kernel) {
this.kernel = kernel;
}

public void setIndentBandwidth(boolean indentBandwidth) {
this.indentBandwidth = indentBandwidth;
}

/**
* <p>Create a new Exporter class instance, holding an array list of export
* statements (i.e., statements with added document information and a hash
Expand Down Expand Up @@ -1716,10 +1731,34 @@ public void computeKernelSmoothedTimeSlices() {
if (this.windowSize % 2 != 0) { // windowSize is the w constant in the paper; only even numbers are acceptable because adding or subtracting w / 2 to or from gamma would not yield integers
this.windowSize = this.windowSize + 1;
}
LocalDateTime firstDate = Exporter.this.filteredStatements.get(0).getDateTime();
LocalDateTime lastDate = Exporter.this.filteredStatements.get(Exporter.this.filteredStatements.size() - 1).getDateTime();
final int W_HALF = windowSize / 2;
LocalDateTime b = this.startDateTime; // start of statement list
LocalDateTime e = this.stopDateTime; // end of statement list
LocalDateTime b = this.startDateTime.isBefore(firstDate) ? firstDate : this.startDateTime; // start of statement list
LocalDateTime e = this.stopDateTime.isAfter(lastDate) ? lastDate : this.stopDateTime; // end of statement list
LocalDateTime gamma = b; // current time while progressing through list of statements
LocalDateTime e2 = e; // indented end point (e minus half w)
if (Exporter.this.indentBandwidth) {
if (timeWindow.equals("minutes")) {
gamma = gamma.plusMinutes(W_HALF);
e2 = e.minusMinutes(W_HALF);
} else if (timeWindow.equals("hours")) {
gamma = gamma.plusHours(W_HALF);
e2 = e.minusHours(W_HALF);
} else if (timeWindow.equals("days")) {
gamma = gamma.plusDays(W_HALF);
e2 = e.minusDays(W_HALF);
} else if (timeWindow.equals("weeks")) {
gamma = gamma.plusWeeks(W_HALF);
e2 = e.minusWeeks(W_HALF);
} else if (timeWindow.equals("months")) {
gamma = gamma.plusMonths(W_HALF);
e2 = e.minusMonths(W_HALF);
} else if (timeWindow.equals("years")) {
gamma = gamma.plusYears(W_HALF);
e2 = e.minusYears(W_HALF);
}
}

// save the labels of the variables and qualifier and put indices in hash maps for fast retrieval
String[] var1Values = extractLabels(Exporter.this.filteredStatements, Exporter.this.variable1, Exporter.this.variable1Document);
Expand Down Expand Up @@ -1750,78 +1789,66 @@ public void computeKernelSmoothedTimeSlices() {
Exporter.this.matrixResults = new ArrayList<>();
if (Exporter.this.kernel.equals("gaussian")) { // for each mid-point gamma, create an empty Matrix and save the start, mid, and end time points in it as defined by the start and end of the whole time range; the actual matrix is injected later
if (timeWindow.equals("minutes")) {
gamma = gamma.minusMinutes(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusMinutes(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusMinutes(1);
}
} else if (timeWindow.equals("hours")) {
gamma = gamma.minusHours(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusHours(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusHours(1);
}
} else if (timeWindow.equals("days")) {
gamma = gamma.minusDays(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusDays(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusDays(1);
}
} else if (timeWindow.equals("weeks")) {
gamma = gamma.minusWeeks(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusWeeks(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusWeeks(1);
}
} else if (timeWindow.equals("months")) {
gamma = gamma.minusMonths(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusMonths(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusMonths(1);
}
} else if (timeWindow.equals("years")) {
gamma = gamma.minusYears(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusYears(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, b, gamma, e));
gamma = gamma.plusYears(1);
}
}
} else { // for each mid-point gamma, create an empty Matrix and save the start, mid, and end time points in it as defined by width w; the actual matrix is injected later
if (timeWindow.equals("minutes")) {
gamma = gamma.minusMinutes(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusMinutes(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusMinutes(W_HALF).isBefore(b) ? b : gamma.minusMinutes(W_HALF), gamma, gamma.plusMinutes(W_HALF).isAfter(e) ? e : gamma.plusMinutes(W_HALF)));
gamma = gamma.plusMinutes(1);
}
} else if (timeWindow.equals("hours")) {
gamma = gamma.minusHours(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusHours(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusHours(W_HALF).isBefore(b) ? b : gamma.minusHours(W_HALF), gamma, gamma.plusHours(W_HALF).isAfter(e) ? e : gamma.plusHours(W_HALF)));
gamma = gamma.plusHours(1);
}
} else if (timeWindow.equals("days")) {
gamma = gamma.minusDays(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusDays(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusDays(W_HALF).isBefore(b) ? b : gamma.minusDays(W_HALF), gamma, gamma.plusDays(W_HALF).isAfter(e) ? e : gamma.plusDays(W_HALF)));
gamma = gamma.plusDays(1);
}
} else if (timeWindow.equals("weeks")) {
gamma = gamma.minusWeeks(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusWeeks(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusWeeks(W_HALF).isBefore(b) ? b : gamma.minusWeeks(W_HALF), gamma, gamma.plusWeeks(W_HALF).isAfter(e) ? e : gamma.plusWeeks(W_HALF)));
gamma = gamma.plusWeeks(1);
}
} else if (timeWindow.equals("months")) {
gamma = gamma.minusMonths(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusMonths(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusMonths(W_HALF).isBefore(b) ? b : gamma.minusMonths(W_HALF), gamma, gamma.plusMonths(W_HALF).isAfter(e) ? e : gamma.plusMonths(W_HALF)));
gamma = gamma.plusMonths(1);
}
} else if (timeWindow.equals("years")) {
gamma = gamma.minusYears(1);
while (gamma.isBefore(e)) {
gamma = gamma.plusYears(1);
while (!gamma.isAfter(e2)) {
Exporter.this.matrixResults.add(new Matrix(var1Values, Exporter.this.networkType.equals("onemode") ? var1Values : var2Values, false, gamma.minusYears(W_HALF).isBefore(b) ? b : gamma.minusYears(W_HALF), gamma, gamma.plusYears(W_HALF).isAfter(e) ? e : gamma.plusYears(W_HALF)));
gamma = gamma.plusYears(1);
}
}
}
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