This package includes a parallel implementation to sample from
Polya-gamma random variables as well as Markov Chain Monte Carlo (MCMC)
code for fitting Bayesian multinomial regression models using MCMC. The
classes of models currently available include multinomial regression
using the pg_lm()
function, multinomial spatial regression using the
pg_splm()
function, multinomial regression with spatially varying
coefficients using the pg_svlm()
function, and spatio-temporal using
the pg_stlm()
function.
There are two options to install the package. You can install the package directly from gitHub or you can clone the package and install locally. The direct installation from gitHub is preferred if you are interested in only using the package and the installation from a cloned gitHub repo is preferred if you are interested in development of the package.
If this is your first time installing this package, make sure you have setup your gitHub personal access token following the instructions below and make sure you have the appropriate compiler.
Direct installation from gitHub is preferred if you are a use of this
package. Once you have setup your gitHub personal access
token and made sure you have the
appropriate compiler, you
can install the devtools
package using
install.packages("devtools")
Once the devtools
library is installed, you can install the pgR
library using
devtools::install_github("jtipton25/pgR")
Note: It is recommended to reguarly check for updates by using
devtools::install_github("jtipton25/pgR")
regularly as this package is
in development and regularly undergoes large changes
Installation from a cloned repository is preferred for those who are actively contributing to package development. To install from a cloned repository, first open the repository on gitHub at https://github.com/jtipton25/pgR. Then click on the clone repository button
and clone copy the output to the clipboard. Then open up a terminal window and type
git clone [email protected]:jtipton25/pgR.git
Once the gitHub repo has finished downloading, open the project in
RStudio by finding and selecting the pgR.Rproj
file
Once the project file has been opened, you can use the build tab to
“Install and Restart” or “More -> Clean and Rebuild” to install the
package. If you add or modify R
code, you can reinstall the updated
package using “Install and Restart”. If you add or modify c++
code
using Rcpp
, use the “More -> Clean and Rebuild” option in the build
tab to recompile the c++
code.
or you can clone the project and install it locally using RStudio.
For either installation method, you will need a personal access token
(PAT) – see here for how to
set this up as this is what I based the following on. It’s pretty
simple, first, make sure the usethis
library is installed using
install.packages("usethis")
and then use
usethis::browse_github_pat()
to open a webpage using your gitHub account. On this webpage is a form to create your PAT with reasonable settings. Give the PAT a nickname and click “Generate token” and the token will be displayed. The token is a string of 40 random letters and digits. Make sure you copy this token to your clipboard as this is the last time you will be able to see it.
Once you have generated a gitHub PAT and copied it to your clipboard, we
will add the PAT to your .Renviron
file. The goal is to add the
following line in your .Renviron
file:
GITHUB_PAT=XXXXX
where the XXXX is the PAT copied from github. The .Renviron
file is a
hidden file that lives in your home directory. If you are comfortable
with the terminal, you can edit this by hand using your favorite text
editor. If you are not comfortable with the terminal, the .Renviron
file can be edited in R
using the usethis
package. In R
type
usethis::edit_r_environ()
Your .Renviron file should pop up in your editor. Add your GITHUB_PAT as above,
GITHUB_PAT=XXXXX
with a line break at the end of the file save the .Renviron
file and
close it. If questioned, YES you do want to use a filename that begins
with a dot .
. Note that, by default, most dotfiles are hidden in the
RStudio file browser, but .Renviron
should always be visible.
Restart R
(Session > Restart R in the RStudio menu bar), as
environment variables are loaded from .Renviron
only at the start of
an R
session. Check that the PAT is now available like so:
usethis::git_sitrep()
You should see the following line in the output:
* Personal access token: '<found in env var>'
Now commands you run from the devtools package, which consults GITHUB_PAT by default, will be able to access private GitHub repositories to which you have access.
-
Linux: It is assumed on Linux systems, the appropriate compiler is available
-
Windows: For Windows, download and install RTools. For R (>=4.0.0) follow the instructions here – older versions of R follow the instructions here.
-
MacOS: If you are on a Mac, make sure you have an openMP supported compiler – see here for instructions on how to get this setup. Follow the instructions for your specific version of R