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Set burnin and credible set size as percentages #9

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Set burnin and credible set size as percentages #9

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45e1e18
Enable setting burn-in and cred. set prob. from command line
May 3, 2017
1f13f85
Burnin is now a percentage
May 3, 2017
c522a92
Credible set size as percentage
May 3, 2017
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8 changes: 4 additions & 4 deletions src/beast/app/tools/SATreeTraceAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@
*/

public class SATreeTraceAnalysis extends TreeTraceAnalysis {

FrequencySet<String> pairs = new FrequencySet<String>();

public SATreeTraceAnalysis(List<Tree> posteriorTreeList, double burninFraction) {
Expand Down Expand Up @@ -79,7 +78,7 @@ public List<String> getNewickTrees () {
* @return a report string
* @throws Exception
*/
public String toReportString(boolean printCladeFrequencies, boolean printPairs, boolean printFrequencies, boolean printTopologyCredibleSet, boolean isHTML) throws Exception {
public String toReportString(boolean printCladeFrequencies, boolean printPairs, boolean printFrequencies, boolean printTopologyCredibleSet, Double credSetProbability, boolean isHTML) throws Exception {
FrequencySet<String> clades = new FrequencySet<String>();
ArrayList<String> tmp = new ArrayList<String>();

Expand Down Expand Up @@ -168,7 +167,7 @@ public String toReportString(boolean printCladeFrequencies, boolean printPairs,
}

if (printTopologyCredibleSet) {
countTopologies(output);
countTopologies(output, credSetProbability);
}

ps.flush();
Expand Down Expand Up @@ -324,8 +323,9 @@ public FrequencySet<String> countSAFrequencies(boolean print, boolean useRanking
/**
*
*/
public void countTopologies(ResultsOutput output) {
public void countTopologies(ResultsOutput output, Double credSetProbability) {
FrequencySet<String> topologies = new FrequencySet<String>();
topologies.setCredSetProbability(credSetProbability);
List<String> trees;
trees = getNewickTrees(true);

Expand Down
26 changes: 24 additions & 2 deletions src/beast/app/tools/SampledAncestorTreeAnalyser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,19 +33,25 @@ public class SampledAncestorTreeAnalyser extends beast.core.Runnable {
private Boolean printCladeFrequencies = false;
private Boolean printTopologyCredibleSet = false;
private Boolean toStandardOutput = true;
private Double credibleSetProportion = 0.95;
private Double burninProportion = 0.1;

public SampledAncestorTreeAnalyser() {}
public SampledAncestorTreeAnalyser(@Param(name="file", description="tree file containing set of ancestral ancestor trees") File file,
@Param(name="burnin", description="percentage of trees to be discarded as burn-in", defaultValue="10.0") Double burninPercentage,
@Param(name="printFrequencies", description="show sampled ancestor frequencies in output table", defaultValue="true") Boolean printFrequencies,
@Param(name="printPairs", description="show ancestor-descendant pair frequencies in output table", defaultValue="false") Boolean printPairs,
@Param(name="printCladeFrequencies", description="show sampled ancestor clade frequencies in output table", defaultValue="false") Boolean printCladeFrequencies,
@Param(name="printTopologyCredibleSet", description="show sampled ancestor tree topology frequencies in output table", defaultValue="false") Boolean printTopologyCredibleSet,
@Param(name="credibleSet", description="percent coverage of the credible set (used for printTopologyCredibleSet)", defaultValue="95.0") Double credibleSetPercentage,
@Param(name="toStandardOutput", description="print to standard output", defaultValue="true") Boolean toStdOut) {
this.file = file;
this.burninProportion = burninPercentage / 100.0;
this.printFrequencies = printFrequencies;
this.printPairs = printPairs;
this.printCladeFrequencies = printCladeFrequencies;
this.printTopologyCredibleSet = printTopologyCredibleSet;
this.credibleSetProportion = credibleSetPercentage / 100.0;
this.toStandardOutput = toStdOut;
}

Expand Down Expand Up @@ -87,7 +93,23 @@ public Boolean getPrintTopologyCredibleSet() {
public void setPrintTopologyCredibleSet(Boolean printTopologyCredibleSet) {
this.printTopologyCredibleSet = printTopologyCredibleSet;
}

public Double getBurnin() {
return this.burninProportion * 100.0;
}

public void setBurnin(Double burnin) {
this.burninProportion = burnin / 100.0;
}

public Double getCredibleSet() {
return this.credibleSetProportion * 100.0;
}

public void setCredibleSet(Double credibleSet) {
this.credibleSetProportion = credibleSet / 100.0;
}

public void run() throws Exception {

FileReader reader = null;
Expand All @@ -96,9 +118,9 @@ public void run() throws Exception {
System.out.println("Reading file " + file.getName());
reader = new FileReader(file);
List<Tree> trees = SATreeTraceAnalysis.Utils.getTrees(file);
SATreeTraceAnalysis analysis = new SATreeTraceAnalysis(trees, 0.1);
SATreeTraceAnalysis analysis = new SATreeTraceAnalysis(trees, burninProportion);

String result = analysis.toReportString(printCladeFrequencies, printPairs, printFrequencies, printTopologyCredibleSet, !toStandardOutput);
String result = analysis.toReportString(printCladeFrequencies, printPairs, printFrequencies, printTopologyCredibleSet, credibleSetProportion, !toStandardOutput);

if (toStandardOutput) {
System.out.println(result);
Expand Down