From 776b782639d868d5fad3d9087dc5720497cf95c9 Mon Sep 17 00:00:00 2001 From: zjzxiaohei <108013625+zjzxiaohei@users.noreply.github.com> Date: Mon, 13 Jan 2025 11:49:36 +1300 Subject: [PATCH] Change the datatype of negr for int to double #56 --- .../readcountmodel/LikelihoodReadCountModel.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/phylonco-beast/src/main/java/phylonco/beast/evolution/readcountmodel/LikelihoodReadCountModel.java b/phylonco-beast/src/main/java/phylonco/beast/evolution/readcountmodel/LikelihoodReadCountModel.java index badbff8..d8e0547 100644 --- a/phylonco-beast/src/main/java/phylonco/beast/evolution/readcountmodel/LikelihoodReadCountModel.java +++ b/phylonco-beast/src/main/java/phylonco/beast/evolution/readcountmodel/LikelihoodReadCountModel.java @@ -44,8 +44,8 @@ public class LikelihoodReadCountModel extends Distribution { private double variance2; private double negp1; private double negp2; - private int negr1; - private int negr2; + private double negr1; + private double negr2; private Double[][] propensities; @@ -117,8 +117,8 @@ public double calculateLogP() { this.variance2 = mean2 + Math.pow(this.alpha2, 2) * vv * Math.pow(sv, 2); this.negp1 = this.mean1 / this.variance1; this.negp2 = this.mean2 / this.variance2; - this.negr1 = Math.round((float) (Math.pow(this.mean1, 2) / (this.variance1 - this.mean1))); - this.negr2 = Math.round((float) (Math.pow(this.mean2, 2) / (this.variance2 - this.mean2))); + this.negr1 = Math.pow(this.mean1, 2) / (this.variance1 - this.mean1); + this.negr2 = Math.pow(this.mean2, 2) / (this.variance2 - this.mean2); for (int j = 0; j < alignmentInput.get().getSiteCount(); j++) {///？ // dirichlet multinomial pmf int patternIndex = alignmentInput.get().getPatternIndex(j); @@ -209,7 +209,7 @@ public double logLiklihoodRC(int genotypeState, int[] readCountNumbers, double w return logLikelihood; } //calculate the probability at each site given read count(coverage)(negative-binomial distribution) - public double logCoverageLikelihood(int[] readCountNumbers, double p, int r) { + public double logCoverageLikelihood(int[] readCountNumbers, double p, double r) { // negative binomial pmf double logCoverageLikelihood; int c = 0;