RSS via MCMC

This page describes how to install the MATLAB scripts that implement the MCMC algorithms to fit the RSS models.

Step 1. Download the repository.

wget https://github.com/stephenslab/rss/archive/master.zip
unzip master.zip
rm master.zip
mv rss-master rss

Step 2. Download and install the lightspeed Matlab toolbox (author: Tom Minka).

cd rss/src
wget http://ftp.research.microsoft.com/downloads/db1653f0-1308-4b45-b358-d8e1011385a0/lightspeed.zip
unzip lightspeed.zip
rm lightspeed.zip
cd lightspeed/
matlab -nodisplay < install_lightspeed.m

Step 3. Download and install the lapack Matlab package (author: Tim Toolan).

cd rss/src
unzip lapack.zip
rm lapackhelp.m lapack.zip license.txt

Notice that if an appropriate compiled version of lapack.c does not exist, the package will ask whether to build one.

Step 4. Download the progress Matlab package (author: Martinho Marta-Almeida).

unzip progress.zip
rm progress.zip license.txt 

Files downloaded from Step 2-4 must be placed under rss/src.

-rw-rw-r-- 1 xiangzhu xiangzhu   5261 2015-11-11 08:46 calc_posterior_bvsr.m
-rw-rw-r-- 1 xiangzhu xiangzhu    972 2015-11-11 08:46 compute_pve.m
-rw-rw-r-- 1 xiangzhu xiangzhu  86772 2015-11-11 12:01 lapack.c
-rw-rw-r-- 1 xiangzhu xiangzhu   5927 2015-11-11 12:01 lapack.m
-rwxrwxr-x 1 xiangzhu xiangzhu 120123 2015-11-11 12:12 lapack.mexa64
drwx------ 6 xiangzhu xiangzhu  32768 2015-11-11 11:54 lightspeed
-rw-rw-r-- 1 xiangzhu xiangzhu   2573 2015-11-11 12:01 progress.m
-rw-rw-r-- 1 xiangzhu xiangzhu   4402 2015-11-11 08:46 propose_gamma.m
-rw-rw-r-- 1 xiangzhu xiangzhu  11629 2015-11-11 08:46 rss_ash.m
-rw-rw-r-- 1 xiangzhu xiangzhu  22182 2015-11-11 08:46 rss_bslmm.m
-rw-rw-r-- 1 xiangzhu xiangzhu   8363 2015-11-11 08:46 rss_bvsr.m
-rw-rw-r-- 1 xiangzhu xiangzhu  11348 2015-11-11 08:46 update_betatilde.m
-rw-rw-r-- 1 xiangzhu xiangzhu   4796 2015-11-11 08:46 update_bz.m
-rw-rw-r-- 1 xiangzhu xiangzhu  17205 2015-11-11 08:46 update_zlabel.m