PhyRPPL: Phylogenetic library for RootPPL

Changelog

v0.7.8

• tooling
• bird filenames

v0.7.7

• graph the net diversification rate
• convert NaN's to -Infinity in the model

v0.7.6

• merged plotting function from the poster prep

v0.7.5

• rootppl now renamed to rppl
• cluster stuff in run_experiments.sh fine-tuned

v0.7.4

• bugfixes in the trees

v0.7.3

New features:

• We support an additional argument whether or not to print the factors along the tree.
• figtree.py post-processing script to color the tree and modifications to runppl.sh to support that automatically. Bugfix:
• correct rotation of bird trees.

v0.7.2

Included the bird supetree as a possible dataset

v0.7.1

Framework supports the rare large shift model now.

v0.7.0

Major update - CombinDS can now run on CUDA as recursion is replaced by iteration.

• Keep the old version of CombineDS that uses recursion just in case.
• Ignore vscode hidden directories.
• simBranch now avoids recursion
• replaces goesUndetected recursion with iteration

v 0.6.5

• Added posterior sampling
• Adapted to new rootppl build system

v.0.6.4

• Improved Python program for posterior analysis includes median, etc.
• New framework for running, which supports better statistics and cluster features.
• Newer version of logz plot.
• Safety improvements to avoid very rare assert (v > 0) error
• Minimum number must be hardcoded, library function application not possible in CUDA.

v0.6.2

• Toolchain improvements.

v0.6.1

• Fixed bugs in the GBM model

v0.6.0

• Geometric Brownian motion added.
• This versions works with the new distributions from phyrppl after LinearNormalInverseGammaNormal was implemented.

v0.5.3

Various small changes, mostly improvements to the script tools.

v0.5.2

• can handle segfaults with runppl.sh

v0.5.1

• improved final sampling
• some tests that lead to discovery of a bug in NomalInverseGammaNormal sampler
• posterior plotting in R improved
• runner script

v0.5.0

• Major bug found, which affected AnaDS1 (not being executed).
• AnaDS-GBM implemented
• Improvements to tools.

v0.4.0

Introduced templates to handle input.

v.0.3.1

Merged CRBD update needed to get same log Z in the CorePPL-TreePPL paper.

v.0.3.0

• Integrated new RootPPL syntax in CombineDS using NEXT
• ANADS - const nu
• conditionOnDetection and posterior sampling to CombineDS

Getting started

Use rootppl to compile an example

rootppl examples/CombineDS.cu

Use program to run the executable

./program

For more details see the miking-dppl/rootppl.