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diff --git a/experiments/README.txt b/experiments/README.txt deleted file mode 100644 index 80f6aa0..0000000 --- a/experiments/README.txt +++ /dev/null @@ -1,47 +0,0 @@ -Description of the files -======================== - -* build_network.py: takes a .csv file containing a criminal network and builds - and extract a compressed binary representation tailored to make the other - scripts faster. - - Takes one argument, the name of the .csv file. The output file has the same - name but the extension .pickle - -* ml.pyx: code to compute the likelihood of a given alpha (time component) and - delta (structural component) for a given infection graph. The optimization of - the beta parameter (probability of being a root) is done internally. - -* process.py: simple loop to do an exhaustive search over a range of alpha - (time component) and delta (structural component). The likelihood (and a few - other things) for each of the values is printed in the file "out.log". - Takes as argument the name of .pickle file computed by build_network.py - Prints columns as alpha, delta, beta, number of roots, likelihood - -* plot3d.py: code to obtain a 3d plot of the log likelihood as a function of - alpha and delta. Can also be easily modified to obtain 2d plots along - specific axes - -Installation -============ - -* most of the code uses standard python + numpy + matplotlib - -* the file ml.pyx is a Cython file which must be compiled in order to be used. -At a high level, ml.pyx is compiled into ml.so. The line "import ml" in -"process.py" will fail if the file ml.so is not present in the directory. -Important: do not forget to recompile ml.pyx after changing it, otherwise you -will be working with an outdated version of ml.so! - -How to compile? A Makefile is provided. If using make on MacOS is too -complicated, it is also possible to compile .pyx files using python distutils -(which I would assume is more standard on MacOS). This only requires distutils -and a simple setup.py file. More details here: -http://docs.cython.org/src/reference/compilation.html#configuring-the-c-build - -Running Code -============ -python build_network.py ../../Results/dag_dat_all.csv -python setup.py build_ext --inplace -python process.py ../../Results/dag_dat_all.pickle -python plot3d.py |