fastcluster: Fast hierarchical clustering routines for R and Python

Copyright © 2011 Daniel Müllner
<http://math.stanford.edu/~muellner>


Installation
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Installation procedures were tested under 64-bit Ubuntu. CRAN also hosts
precompiled binaries (of the R library, not the Python module) for Windows and
MacOS X. In principle, it should be possible to install the fastcluster package
on any system that has a C++ compiler and R respectively Python with
NumPy. There are no unusual libraries needed to compile the package, only the
STL library, which every C++ compiler should have by default.

Please send me feedback if you accomplish to install the fastcluster package on
a different platform or if you needed to tweak the configuration! I will the
update the installation instructions and modify the package if needed
(eg. include the right compiler flags for various operating systems).


Installation for R
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Enter the command install.packages("fastcluster") in R, and R will download the package automatically, then install it. That's it!

If this does not work, please consult R's help function by typing ?INSTALL from within R or read the “R installation and administration” manual:

    http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages

For manual download, you can get the fastcluster package from the download page at CRAN:

    http://cran.r-project.org/web/packages/fastcluster/

You may need to start R with administrator rights to be able to install packages. There are ways to install R packages without administrator privileges in your user directories. See this help page for example:

  http://csg.sph.umich.edu/docs/R/localpackages.html


Installation for Python
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Make sure that you have Python and NumPy installed. If you have not done so
already, download the fastcluster package from the R archive here:

    http://cran.r-project.org/web/packages/fastcluster/

Open a terminal, go to the directory with the downloaded file and extract the
contents of the archive with:

    tar -xvf fastcluster_(version).tar.gz

Alternatively, use your favorite archive manager for unpacking, eg. on
Windows. This will generate a new directory fastcluster. Switch to its python
subdirectory:

    cd fastcluster/python/

Now compile and install the Python module by:

    python setup.py install

Again, you may need to precede this command with sudo or install the package in
your home directory. For example, the line

    python setup.py install --home=~

installs the package in the path lib/python/ under your home directory. See the
chapter “Installing Python modules” in the Python documentation for further
help.
