a Python package to test for Unified Neutral Theory of Biodiversity and biogeography in Large dataset. EcoloPy deal with species abundance and diversity data. It allows to fit this data into ecological models and implements some statistical tests. It is able to deal with large dataset like genetic element content of mammalian genomes.
The package was implemented in the context of a study of the distribution of genetic elements in Eukaryotic genomes [Serra2013].
http://fransua.github.io/ecolopy/
Please refer to the following article if you use this package to analyze or process results that are part of a published work:
Serra, F., Becher, V., & Dopazo, H. (2013). Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes. PloS One, 8(6), e63915. doi:10.1371/journal.pone.0063915
This is to install python packages easily.
sudo apt-get install python-setuptools
cd /tmp/ wget http://www.mpfr.org/mpfr-current/mpfr-3.1.2.tar.gz tar xzvf mpfr-3.1.2.tar.gz cd mpfr-3.1.2/ ./configure make make check sudo make install
cd /tmp/ wget ftp://ftp.gmplib.org/pub/gmp/gmp-5.1.2.tar.bz2 tar xjvf gmp-5.1.2.tar.bz2 cd gmp-5.1.2/ ./configure make make check sudo make install
http://www.multiprecision.org/
cd /tmp/ wget http://www.multiprecision.org/mpc/download/mpc-1.0.1.tar.gz tar xzvf mpc-1.0.1.tar.gz cd mpc-1.0.1/ ./configure make make check sudo make install
for huge numbers.
sudo apt-get install python2.7-dev libmpfr-dev libgmp3-dev libmpc-dev sudo easy_install gmpy2
for optimization of log likelihood
sudo easy_install scipy
sudo easy_install numpy
Not compulsory, only to draw graphs
sudo easy_install matplotlib
sudo python setup.py install
test usage:
python test_all.py full
- do something with metacommunity
Broken -> problem with scipy install at travis.