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Merged
walterxie merged 6 commits into from
Oct 6, 2026
Merged

ensure true=1 false=0 when converting a boolean column #177 #178

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9d403f1
ensure true=1 false=0 when convert a boolean column
EvaLiyt Sep 30, 2026
4430526
set booleans also compute median hpd ess etc as integer for not throw…
EvaLiyt Oct 4, 2026
fc4bdaf
clean up the code to do the smallest changes
EvaLiyt Oct 5, 2026
22dbb1e
clean up the code and ignore case issue for true and false
EvaLiyt Oct 5, 2026
c42aa1d
Merge branch 'CompEvol:master' into master
EvaLiyt Oct 6, 2026
9e5b00c
remove unnecessary check
EvaLiyt Oct 6, 2026
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47 changes: 26 additions & 21 deletions beast-fx/src/main/java/beastfx/app/tools/LogAnalyser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -250,21 +250,29 @@ protected void readLogFile(String fileName, int burnInPercentage) throws IOExcep
if (str.indexOf('#') < 0 && str.matches("[-0-9].*"))
if (++data >= 0 && data < m_fTraces[0].length)
for (String str2 : str.split("\\s")) {
try {
if (str2.indexOf('.') >= 0) {
m_types[i] = type.REAL;
if ("true".equalsIgnoreCase(str2) || "false".equalsIgnoreCase(str2)) {
// set true = 1 false = 0
m_types[i] = type.BOOL;
m_fTraces[i][data] = str2.equals("true") ? 1.0 : 0.0;
i++;
} else {
try {
if (str2.indexOf('.') >= 0) {
m_types[i] = type.REAL;
}
m_fTraces[i][data] = Double.parseDouble(str2);
} catch (Exception e) {

if (m_ranges[i] == null) {
m_ranges[i] = new ArrayList<>();
}
if (!m_ranges[i].contains(str2)) {
m_ranges[i].add(str2);
}
m_fTraces[i][data] = 1.0 * m_ranges[i].indexOf(str2);
}
m_fTraces[i][data] = Double.parseDouble(str2);
} catch (Exception e) {
if (m_ranges[i] == null) {
m_ranges[i] = new ArrayList<>();
}
if (!m_ranges[i].contains(str2)) {
m_ranges[i].add(str2);
}
m_fTraces[i][data] = 1.0 * m_ranges[i].indexOf(str2);
i++;
}
i++;
}
while (reported < 81 && 1000.0 * reported < 81000.0 * (data + 1)/ total) {
log("*");
Expand All @@ -274,12 +282,9 @@ protected void readLogFile(String fileName, int burnInPercentage) throws IOExcep
logln("");
// determine types
for (int i = 0; i < items; i++)
if (m_ranges[i] != null)
if (m_ranges[i].size() == 2 && m_ranges[i].contains("true") && m_ranges[i].contains("false") ||
m_ranges[i].size() == 1 && (m_ranges[i].contains("true") || m_ranges[i].contains("false")))
m_types[i] = type.BOOL;
else
m_types[i] = type.NOMINAL;
if (m_ranges[i] != null && (! m_types[i].equals(type.BOOL)) ) {
m_types[i] = type.NOMINAL;
}

fin.close();
} // readLogFile
Expand Down Expand Up @@ -323,8 +328,8 @@ public void calcStats(String [] tags) {
m_fStdDev[i] = Double.NaN;
}

if (m_types[i] == type.REAL || m_types[i] == type.INTEGER) {
// calc median, and 95% HPD interval
if (m_types[i] == type.REAL || m_types[i] == type.INTEGER || m_types[i] == type.BOOL) {
// calc median, and 95% HPD interval (BOOL traces are true = 1, false = 0)
Double[] sorted = trace.clone();
Arrays.sort(sorted);
m_fMedian[i] = sorted[trace.length / 2];
Expand Down
96 changes: 96 additions & 0 deletions beast-fx/src/test/java/test/beastfx/app/tools/LogAnalyserTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
package test.beastfx.app.tools;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;

import org.junit.jupiter.api.Test;

import beastfx.app.tools.LogAnalyser;

import static org.junit.jupiter.api.Assertions.*;

public class LogAnalyserTest {

/** writes a trace log with the given rows under the header Sample, x, y, z */
private static File log(String... rows) throws IOException {
File file = File.createTempFile("LogAnalyserTest", ".log");
file.deleteOnExit();
StringBuilder b = new StringBuilder("Sample\tx\ty\tz\n");
for (String row : rows) {
b.append(row).append('\n');
}
Files.writeString(file.toPath(), b.toString());
return file;
}

/**
* Boolean columns must read as true = 1 and false = 0, whichever value appears first.
*/
@Test
void testBooleansAreOneAndZero() throws IOException {
LogAnalyser analyser = new LogAnalyser(log(
"0\ttrue\tfalse\tA",
"1\tfalse\ttrue\tB",
"2\tfalse\ttrue\tA",
"3\tfalse\ttrue\tA").getPath(), 0, true, true);

// starts with true
assertArrayEquals(new Double[] {1.0, 0.0, 0.0, 0.0}, analyser.getTrace("x"));
assertEquals(0.25, analyser.getMean("x"), 1e-12);
// starts with false
assertArrayEquals(new Double[] {0.0, 1.0, 1.0, 1.0}, analyser.getTrace("y"));
assertEquals(0.75, analyser.getMean("y"), 1e-12);
// other nominal values are still numbered in order of first appearance
assertArrayEquals(new Double[] {0.0, 1.0, 0.0, 0.0}, analyser.getTrace("z"));
}

/** the same holds when burn-in removes the first rows */
@Test
void testBooleansAfterBurnIn() throws IOException {
LogAnalyser analyser = new LogAnalyser(log(
"0\tfalse\tfalse\tA",
"1\ttrue\tfalse\tA",
"2\tfalse\ttrue\tA",
"3\ttrue\ttrue\tA",
"4\ttrue\ttrue\tA",
"5\tfalse\ttrue\tA",
"6\ttrue\ttrue\tA",
"7\ttrue\ttrue\tA",
"8\ttrue\ttrue\tA",
"9\ttrue\ttrue\tA").getPath(), 10, true, true);

// burn-in 10% drops row 0; x now starts with true
assertArrayEquals(new Double[] {1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0, 1.0, 1.0}, analyser.getTrace("x"));
// y: one false, then eight true
assertEquals(8.0 / 9.0, analyser.getMean("y"), 1e-12);
}

/**
* A boolean column gets every statistic, the same as the 1/0 column it stands for:
* x is true/false, y the same values as 1/0.
*/
@Test
void testBooleanStatsMatchOneZero() throws IOException {
String[] rows = new String[200];
java.util.Random random = new java.util.Random(1);
boolean on = true;
for (int k = 0; k < rows.length; k++) {
if (random.nextDouble() < 0.2) {
on = !on;
}
rows[k] = (k * 1000) + "\t" + on + "\t" + (on ? 1 : 0) + "\t" + random.nextDouble();
}
LogAnalyser analyser = new LogAnalyser(log(rows).getPath(), 10, true, true);

assertEquals(analyser.getMean("y"), analyser.getMean("x"), 1e-12);
assertEquals(analyser.getStdError("y"), analyser.getStdError("x"), 1e-12);
assertEquals(analyser.getStdDev("y"), analyser.getStdDev("x"), 1e-12);
assertEquals(analyser.getMedian("y"), analyser.getMedian("x"), 1e-12);
assertEquals(analyser.get95HPDlow("y"), analyser.get95HPDlow("x"), 1e-12);
assertEquals(analyser.get95HPDup("y"), analyser.get95HPDup("x"), 1e-12);
assertEquals(analyser.getACT("y"), analyser.getACT("x"), 1e-12);
assertEquals(analyser.getESS("y"), analyser.getESS("x"), 1e-12);
assertFalse(Double.isNaN(analyser.getESS("x")));
}
}