First steps with FFPopSim

FFPopSim is supposed to be easy to use. This page is meant to help new users to familiarize themselves with the library by means of examples. For a complete reference of classes and functions, please see the Contents page.

For the impatient ones...

An effective way to discover all available methods is to import FFPopSim from the iPython interactive shell, create a population, and use TAB autocompletion:

In [1]: import FFPopSim as h
In [2]: pop = h.haploid_lowd(5)   #create a population with 5 loci
In [3]: pop.      <--- TAB

Importing FFPopSim

FFPopSim is a single Python module. As such, you can import it with the python import statement, provided the files FFPopSim.py and _FFPopSim.so are in a folder in your PYTHONPATH. If you wish to perform a system-wide installation of FFPopSim, call the make recipe python-install as a superuser:

$ sudo make python-install

Note

if this sounds new to you, just put those two files into your current directory, from which you plan to call the Python interpreter. import statements first look in the current folder for modules.

We recommend to import Numpy and matplotlib together with FFPopSim. In short, all your scripts should begin with the following piece of code:

import numpy as np
import matplotlib.pyplot as plt
import FFPopSim

The selective import of parts of FFPopSim using from FFPopSim import <xxx> is discouraged and its results are untested.

Examples

See the main page for examples.

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