pydt

Pitman Yor diffusion tree sampler

To compile you will need the Boost libraries. e.g. if boost is in ~/boost_1_51_0/ then run:

g++ -O3 main.cpp -I ~/boost_1_51_0/ -o pydt

To run on the CCLE data provided here you can then run for example

./pydt 0 1.5 sensitivity.txt cell_names.txt 1000 1 1

Just running pydt with no args will explain what these inputs are.

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
GaussianVector.hpp		GaussianVector.hpp
Makefile		Makefile
README.md		README.md
Settings.hpp		Settings.hpp
Tree.hpp		Tree.hpp
TreeNode.hpp		TreeNode.hpp
VectorExtensions.hpp		VectorExtensions.hpp
cell_names.txt		cell_names.txt
collate.R		collate.R
drug_names.txt		drug_names.txt
gddt.py		gddt.py
getting_it_right.R		getting_it_right.R
getting_it_right2.R		getting_it_right2.R
kingman.hpp		kingman.hpp
main.cpp		main.cpp
perm_targets.R		perm_targets.R
plotDepthVsN.R		plotDepthVsN.R
plotHist.R		plotHist.R
plotKingman.R		plotKingman.R
plot_ddt.py		plot_ddt.py
pydtsamplers.hpp		pydtsamplers.hpp
read_file.cpp		read_file.cpp
run.sh		run.sh
sensitivity.txt		sensitivity.txt
slice_sample.hpp		slice_sample.hpp
test_slice_idea.m		test_slice_idea.m

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