diff --git a/build.xml b/build.xml index 82691a4..f826aab 100644 --- a/build.xml +++ b/build.xml @@ -8,21 +8,21 @@ - - - - + + + + + + + + - - - - @@ -31,22 +31,27 @@ - - + - - - + - + - + - + + + + ** Required file version.xml does not exist. ** + + + + + @@ -85,9 +90,7 @@ fork="true" memoryinitialsize="256m" memorymaximumsize="256m"> - - + @@ -99,37 +102,11 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + @@ -137,7 +114,7 @@ - + @@ -193,7 +170,7 @@ - + @@ -207,17 +184,16 @@ - - - + + - + - + diff --git a/examples/NS_4taxa_NormalBirthRate.xml b/examples/NS_4taxa_NormalBirthRate.xml index edc2f59..ada7abb 100644 --- a/examples/NS_4taxa_NormalBirthRate.xml +++ b/examples/NS_4taxa_NormalBirthRate.xml @@ -1,4 +1,4 @@ - + beast.math.distributions.Uniform -beast.math.distributions.Exponential -beast.math.distributions.LogNormalDistributionModel -beast.math.distributions.Normal -beast.math.distributions.Beta -beast.math.distributions.Gamma -beast.math.distributions.LaplaceDistribution -beast.math.distributions.Prior -beast.math.distributions.InverseGamma -beast.math.distributions.OneOnX +beast.base.inference.distribution.Uniform +beast.base.inference.distribution.Exponential +beast.base.inference.distribution.LogNormalDistributionModel +beast.base.inference.distribution.Normal +beast.base.inference.distribution.Beta +beast.base.inference.distribution.Gamma +beast.base.inference.distribution.LaplaceDistribution +beast.base.inference.distribution.Prior +beast.base.inference.distribution.InverseGamma +beast.base.inference.distribution.OneOnX 0.25 - + 1.0 - - - + + + - + - + @@ -87,7 +87,7 @@ ML: -2349.814260249774 Information: 14.442480805674677 (SD ~ 0.12) - + 1.0 @@ -97,7 +97,7 @@ ML: -2349.814260249774 Information: 14.442480805674677 (SD ~ 0.12) - + 1.0 @@ -131,7 +131,7 @@ ML: -2349.814260249774 Information: 14.442480805674677 (SD ~ 0.12) - + @@ -147,7 +147,7 @@ ML: -2349.814260249774 Information: 14.442480805674677 (SD ~ 0.12) - + diff --git a/examples/dna.xml b/examples/dna.xml index 7494f18..b0d3258 100644 --- a/examples/dna.xml +++ b/examples/dna.xml @@ -1,4 +1,4 @@ - + -beast.math.distributions.Uniform -beast.math.distributions.Exponential -beast.math.distributions.LogNormalDistributionModel -beast.math.distributions.Normal -beast.math.distributions.Beta -beast.math.distributions.Gamma -beast.math.distributions.LaplaceDistribution -beast.math.distributions.Prior -beast.math.distributions.InverseGamma -beast.math.distributions.OneOnX +beast.base.inference.distribution.Uniform +beast.base.inference.distribution.Exponential +beast.base.inference.distribution.LogNormalDistributionModel +beast.base.inference.distribution.Normal +beast.base.inference.distribution.Beta +beast.base.inference.distribution.Gamma +beast.base.inference.distribution.LaplaceDistribution +beast.base.inference.distribution.Prior +beast.base.inference.distribution.InverseGamma +beast.base.inference.distribution.OneOnX