Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
Jags Wald module
Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Failed to load latest commit information.|
JAGS Wald module ================ Provides shifted Wald (Inverse Gaussian) distribution functions for JAGS. JAGS Extensions provided ------------------------ Distributions """"""""""""" - dswald: Shifted Wald distribution - dswtn: Shifted Wald distribution with across-trial variability in the Wald drift rate parameter governed by a truncated normal distribution Functions """"""""" - dswald: Shifted Wald density function - pswald: Shifted Wald cumulative density function Abandoned Functionality """"""""""""""""""""""" - dswgam: Shifted Wald distribution with across-trial variability in the Wald drift rate parameter governed by a gamma distribution. This function was abandoned due to various reasons. However, the examples provided show how this can be implemented using a for-loop construction. Examples -------- The examples/SWmixturesCode directory contains all files that are necessary to fit the SW-TN and SW-GAM mixtures as described in Steingroever, Wabersich, & Wagenmakers (submitted). R and JAGS are necessary to fit the models. 1. Fit_IG_TN_ind.r: R code to generate data and to fit the IG-TN mixture. 2. Fit_IG_GAM_ind.r: R code to generate data and to fit the IG-GAM mixture. 3. Model_IG_TN_ind.txt: JAGS model file of the IG-TN mixture. This file is needed to run the Fit_IG_TN_ind.r code. 4. Model_IG_GAM_ind.txt: JAGS model file of the IG-GAM mixture. This file is needed to run the Fit_IG_GAM_ind.r code. Please note ----------- When using this code or module, please cite as: Steingroever, Wabersich, & Wagenmakers (submitted). Modeling Across-Trial Variability in the Wald Drift Rate Parameter. License ------- http://www.r-project.org/Licenses/GPL-2 Installation ------------ Linux and Mac """"""""""""" Use the tarball and install as usual: ./configure && make && sudo make install Note: It might be necessary to define a different prefix, depending on where JAGS is copied (i.e. installed), for example: ./configure --prefix /usr && make && sudo make install Windows """"""" For Windows we provide precompiled binaries, which come with an installer. See the releases page for the Windows installer. Compiling from a cloned repository ---------------------------------- # dependencies (on a clean ubuntu installation) sudo apt-get install autoconf automake libtool g++ # creating all auxiliary files autoreconf -fvi # building ./configure make # or, if JAGS has been installed in a different location, e.g. /usr ./configure --prefix /usr make # install sudo make install Windows Compiling """"""""""""""""" **First, in Linux:** - For building the module in Windows, it is easiest to use a tarball that was created in linux like this (starting from a source clone): autoreconf -fvi ./configure make dist-gzip - As an alternative to building this tarball yourself from the github source, one can use the tarball that is available for the latest release. - Copy the *.tar.gz file to your msys home directory and continue from there. **Second, in Windows:** - Install MinGW (MinGW installer including msys): http://www.mingw.org In MinGW get installer: msys-base is all you need. - Install TDM-GCC Compiler Suite: http://tdm-gcc.tdragon.net Use the exact same version of tdm-gcc as has been used to compile your JAGS Version on your system. In that case, also don't forget to untick the "Check for updated files on the TDM-GCC server" during the installation proccess of tdm-gcc. For Jags-4.0.0 and Jags-4.1.0 use: tdm64-gcc-4.6.1.exe For Jags-4.2.0 use: tdm64-gcc-4.9.2-3.exe - Delete all *.dll.a files int the TDM-GCC Installation, so the compiler will link to the static libraries. - Change path in c:/mingw/msys/1.0/etc/fstab from this: c:/mingw /mingw to: c:/MinGW64 /mingw to use TDM-GCC compilers - Alternatively to TDM-GCC, you could also use Rtools (https://cran.r-project.org/bin/windows/Rtools/). For Jags-4.2.0 use: Rtools33.exe Change path in c:/mingw/msys/1.0/etc/fstab to: C:/Rtools/mingw_64 /mingw to use Rtools compilers - --> Start msys, extract tarball in your home dir, cd into dir and do the following: - *Note*: the module needs the JAGS include files and the JAGS libraries. Therefore use the -L and -I options, as shown below. - For building 32bit binaries: CXX="g++ -m32" \ ./configure LDFLAGS="-L/c/Progra~1/JAGS/JAGS-4.2.0/i386/bin" CXXFLAGS="-I/c/Progra~1/JAGS/JAGS-4.2.0/include" make win32-install - For building 64bit binaries: CXX="g++ -m64" \ ./configure LDFLAGS="-L/c/Progra~1/JAGS/JAGS-4.2.0/x64/bin" CXXFLAGS="-I/c/Progra~1/JAGS/JAGS-4.2.0/include" make win64-install - Copy the win/win32/wald.* or win/win64/wald.* files to your JAGS modules directory to enable the module. For JAGS-4.2.0 this usually is: x64: C:\Program Files\JAGS\JAGS-4.2.0\x64\modules x32: C:\Program Files\JAGS\JAGS-4.2.0\x32\modules - *Note*: If you compile both 32bit and 64bit don't forget to make clean between the building. - *All Windows commands in one* (for copy paste convenience) CXX="g++ -m32" \ ./configure LDFLAGS="-L/c/Progra~1/JAGS/JAGS-4.2.0/i386/bin" \ CXXFLAGS="-I/c/Progra~1/JAGS/JAGS-4.2.0/include" && \ make win32-install && \ make clean && \ CXX="g++ -m64" \ ./configure LDFLAGS="-L/c/Progra~1/JAGS/JAGS-4.2.0/x64/bin" \ CXXFLAGS="-I/c/Progra~1/JAGS/JAGS-4.2.0/include" && make win64-install && \ make clean