The easiest way to install the package is with
install.packages("diversitree")
which will get the most recent version from CRAN. However, this is sometimes out of date, as I don't put every version up there. In that case, you will probably have to install from source.
In between releases on the diversitree website (and the less frequent CRAN releases), bleeding-edge versions of diversitree can be obtained from github:
git clone git://github.com/richfitz/diversitree.git
Which will create a directory diversitree. From
within the diversitree/diversitree directory, run
autoheader autoconf
to generate the configure script. From within the
diversitree directory,
R CMD INSTALL diversitree
or
R CMD INSTALL diversitree --configure-args='--with-fftw=/path/to/fftw'
QuaSSE requires that the fftw (Fastest Fourier Transforms in the West) libraries are installed. If you want to use QuaSSE, before installing diversitree, download and install fftw. If you install fftw in a different location than a "standard" location (i.e., somewhere that your C compiler will find headers and libraries automatically) you have to tell the compilers where it is:
R CMD INSTALL diversitree --configure-args='--with-fftw=/path/to/fftw'
where the path will be the path so that the files
/path/to/fftw/include/fftw3.h /path/to/fftw/lib/lib/fftw3.so
exist. When installing, look for a line that says
Using fftw for QuaSSE FFT calculations
in the output. If you see
configure: WARNING: No fftw found - QuaSSE/fftC will not be available
then diversitree could not find the fftw libraries.
On Windows, set the environment variable
LIB_FFTW to point to the directory that contains
include/fftw.h, and install the package. Far less
checking is done when installing on windows, due to limitations
with the build system there. As I don't have a windows system
at present, I cannot test this, and am only assured that it
works. Alternatively, email me if the CRAN version is out of
date, and I can arrange to have a binary package built for you.