From 30f258221df308f1acc0057ec723230affb3d25b Mon Sep 17 00:00:00 2001 From: Chi Zhang Date: Tue, 5 Jul 2016 11:47:55 +0200 Subject: [PATCH 1/2] solved conflict about the new parameterization --- src/beast/evolution/speciation/BirthDeathSkylineModel.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/beast/evolution/speciation/BirthDeathSkylineModel.java b/src/beast/evolution/speciation/BirthDeathSkylineModel.java index 8e83f6a..0718f65 100644 --- a/src/beast/evolution/speciation/BirthDeathSkylineModel.java +++ b/src/beast/evolution/speciation/BirthDeathSkylineModel.java @@ -101,9 +101,9 @@ public class BirthDeathSkylineModel extends SpeciesTreeDistribution { new Input("contemp", "Only contemporaneous sampling (i.e. all tips are from same sampling time, default false)", false); public Input R0 = - new Input("R0", "The basic reproduction number", Input.Validate.XOR, birthRate); + new Input("R0", "The basic reproduction number"); public Input becomeUninfectiousRate = - new Input("becomeUninfectiousRate", "Rate at which individuals become uninfectious (throuch recovery or sampling)", Input.Validate.XOR, deathRate); + new Input("becomeUninfectiousRate", "Rate at which individuals become uninfectious (throuch recovery or sampling)"); public Input samplingProportion = new Input("samplingProportion", "The samplingProportion = samplingRate / becomeUninfectiousRate", Input.Validate.XOR, samplingRate); From 8ee4cd546ca32abf6fb652fc0a48ee774a078dbe Mon Sep 17 00:00:00 2001 From: Chi Zhang Date: Wed, 6 Jul 2016 09:04:57 +0200 Subject: [PATCH 2/2] another try to solve conflict about the new parameterization --- .../evolution/speciation/BirthDeathSkylineModel.java | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/beast/evolution/speciation/BirthDeathSkylineModel.java b/src/beast/evolution/speciation/BirthDeathSkylineModel.java index 0718f65..52c46e6 100644 --- a/src/beast/evolution/speciation/BirthDeathSkylineModel.java +++ b/src/beast/evolution/speciation/BirthDeathSkylineModel.java @@ -105,14 +105,10 @@ public class BirthDeathSkylineModel extends SpeciesTreeDistribution { public Input becomeUninfectiousRate = new Input("becomeUninfectiousRate", "Rate at which individuals become uninfectious (throuch recovery or sampling)"); public Input samplingProportion = - new Input("samplingProportion", "The samplingProportion = samplingRate / becomeUninfectiousRate", Input.Validate.XOR, samplingRate); - - public Input netDiversification = - new Input("netDiversification", "Net diversification rate", Input.Validate.XOR, birthRate); - public Input turnOver = - new Input("turnOver", "Turn over rate", Input.Validate.XOR, deathRate); - // public Input samplingProportion = - // new Input("samplingProportion", "Sampling proportion", Input.Validate.XOR, samplingRate); + new Input("samplingProportion", "The samplingProportion = samplingRate / becomeUninfectiousRate"); + + public Input netDiversification = new Input("netDiversification", "Net diversification rate"); + public Input turnOver = new Input("turnOver", "Turn over rate"); public Input forceRateChange = new Input("forceRateChange", "If there is more than one interval and we estimate the time of rate change, do we enforce it to be within the tree interval? Default true", true);