Coalescent simulations in continuous space
Project description
Simulates the coalescent for populations evolving in a spatial continuum under the extinction/recolonisation model. The simulations support:
A sample of n individuals with m loci at arbitrary locations on a torus of diameter L.
Arbitrary recombination rates between adjacent loci.
An arbitrary number of classes of event occuring at fixed rates.
Ercs supports both Python 2 and 3.
Documentation
Here’s a quick example for the impatient:
import ercs sim = ercs.Simulator(10) sim.sample = [None, (3, 2), (6, 4), (7, 0)] sim.event_classes = [ercs.DiscEventClass(u=0.5, r=1)] pi, tau = sim.run(1)
Full documentation for ercs is available at http://jeromekelleher.github.com/ercs.
Installation
Ercs depends on the GNU Scientific Library, which must be installed before the ercs module can be built. Fortunately, this is straightforward on most platforms. For example, on Debian or Ubuntu use:
$ sudo apt-get install libgsl0-dev
or on Fedora:
$ sudo yum install gsl-devel
GSL is available on most packaging systems; if it is not available on your platform, it can be installed from source.
Once GSL has been installed we can build the ercs module using the standard Python methods. For example, using pip we have
$ sudo pip install ercs
Or, we can manually download the package, unpack it and then run:
$ python setup.py build $ sudo python setup.py install
Most of the time this will compile and install the module without difficulty.
It is also possible to download the latest development version of ercs from github.
Potential problems
On platforms that GSL is not available as part of the native packaging system (or GSL was installed locally because of non-root access) there can be issues with finding the correct headers and libraries when compiling ercs. For example, on FreeBSD we get something like this:
$ python setup.py build ... [Messages cut for brevity] ... In file included from _ercsmodule.c:27: lib/ercs.h:26:25: error: gsl/gsl_rng.h: No such file or directory In file included from _ercsmodule.c:27: lib/ercs.h:73: error: expected declaration specifiers or '...' before 'gsl_rng' lib/ercs.h:94: error: expected specifier-qualifier-list before 'gsl_rng' _ercsmodule.c: In function 'pyercs_simulate': _ercsmodule.c:351: error: 'ercs_t' has no member named 'pi' _ercsmodule.c:356: error: 'ercs_t' has no member named 'tau' error: command 'cc' failed with exit status 1
This can be remedied by using the gsl-config program to set the the LDFLAGS and CFLAGS environment variables to their correct values:
$ CFLAGS=`gsl-config --cflags` LDFLAGS=`gsl-config --libs` python setup.py build
Tests
Ercs provides some test cases to ensure that the installation has gone smoothly. It is a good idea to run these immediately after installation:
$ python tests.py
It is also possible to run some tests on the low-level C library. To do this, cd to the lib directory and run:
$ make check
This will build the C library test cases and run them. If compilation fails, it may be necessary set LDFLAGS and CFLAGS as before:
$ make CFLAGS="`gsl-config --cflags`" LDFLAGS="`gsl-config --libs`" check
Tested platforms
Ercs has been successfully built and tested on the following platforms:
Operating system |
Platform |
Python |
Compiler |
|---|---|---|---|
Ubuntu 8.04 |
i386 |
2.5.2 |
gcc 4.2.3 |
NetBSD 5.0 |
i386 |
2.7.3 |
gcc 4.1.3 |
Fedora 17 |
i386 |
2.7.3 |
gcc 4.7.2 |
Fedora 17 |
i386 |
3.2.3 |
gcc 4.7.2 |
Cygwin |
i386 |
2.6.8 |
gcc 4.5.3 |
Ubuntu 12.04 |
x86-64 |
2.7.3 |
gcc 4.6.3 |
Ubuntu 12.04 |
x86-64 |
3.2.3 |
gcc 4.6.3 |
FreeBSD 9.0 |
i386 |
3.2.2 |
gcc 4.2.2 |
FreeBSD 9.0 |
i386 |
2.7.2 |
gcc 4.2.2 |
FreeBSD 9.0 |
i386 |
3.1.4 |
clang 3.0 |
Solaris 11 |
x86-64 |
2.6.4 |
Sun C 5.12 |
Mac OSX 10.6.8 |
x86-64 |
2.6.1 |
gcc 4.2.1 |
Mac OSX 10.6.8 |
x86-64 |
3.2.3 |
gcc 4.2.1 |
Mac OS X 10.4.11 |
ppc |
3.2.3 |
gcc 4.0.1 |
Mac OS X 10.4.11 |
ppc |
2.7.3 |
gcc 4.0.1 |
Debian wheezy |
armv6l |
2.7.3 |
gcc 4.6.3 |
Debian squeeze |
ppc64 |
2.6.6 |
gcc 4.4.5 |
Debian squeeze |
ppc64 |
3.1.3 |
gcc 4.4.5 |
The C library has additionally been compiled and tested with the following processors and compilers:
Platform |
Compiler |
|---|---|
Linux 2.6.18-164.15.1.el5 x86_64 GNU/Linux |
Intel(R) C 11.0 |
Linux 2.6.32-5-amd64 x86_64 GNU/Linux |
gcc 4.4.5 |
Linux 2.6.32-5-amd64 x86_64 GNU/Linux |
clang 1.1 |
Linux 3.2.0-32-generic x86_64 GNU/Linux |
gcc 4.6.3 |
Linux 3.2.0-32-generic x86_64 GNU/Linux |
clang 3.0 |
Linux 3.2.27+ armv6l GNU/Linux |
gcc 4.6.3 |
Linux 2.6.32-5-powerpc64 ppc64 GNU/Linux |
gcc 4.4.5 |
Linux 2.6.32-5-powerpc64 ppc64 GNU/Linux |
clang 1.1 |
SunOS 5.11 11.0 i86pc i386 i86pc |
Sun C 5.12 |
SunOS 5.10 sun4u sparc SUNW,Ultra-4 |
Sun C 5.8 |
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