The goal of pg is to provide both R and C++ header access to the Polya Gamma distribution sampling routine.
InstallationYou can install the development version of pg
from GitHub with:
# install.packages("devtools")
devtools::install_github("tmsalab/pg")
Usage
Let X
be a Polya Gamma Distribution denoted by PG(h, z)
, where h
is the âshapeâ parameter and z
is the âscaleâ parameter. Presently, the following sampling cases are enabled:
h > 170
: Normal approximation methodh <= 170
and h > 13
: Saddlepoint methodh = 1
or h = 2
: Devroye methodh > 0
: Sum of gammas method.h < 0
: Result is automatically set to zero.Not implemented:
h <= 13
and h > 1
: Alternative method (waiting for verification)The package structure allows for the sampling routines to be accessed either via C++ or through R. The return type can be either a single value or a vector. When repeat sampling is needed with the same b
and c
, please use the vectorized sampler.
Using the sampling routine in C++ through a standalone .cpp
file requires either the rpg_scalar_hybrid()
, rpg_vector_hybrid()
, or rpg_hybrid()
function to be accessed in the pg
C++ namespace. Each of these functions will automatically select the appropriate algorithm based on criteria discussed previously.
#include <pg.h>
// [[Rcpp::depends(RcppArmadillo, pg)]]
// [[Rcpp::export]]
double rpg_scalar(const double h, const double z) {
return pg::rpg_scalar_hybrid(h, z);
}
// [[Rcpp::export]]
arma::vec rpg_hybrid(const arma::vec& h, const arma::vec& z) {
return pg::rpg_hybrid(h, z);
}
// [[Rcpp::export]]
arma::vec rpg_vector(unsigned int n, const double h, const double z) {
return pg::rpg_vector_hybrid(n, h, z);
}
For use within an R package, include a the pg
package name in the DESCRIPTION
file. From there, include the pg.h
header in a similar manner to the stand-alone C++ example.
LinkingTo:
Rcpp,
RcppArmadillo
pg
Sampling with R
For use within an R file, you can do:
# Number of observations to sample
n = 4
# Select the PG(h, z) values
h = 1; z = 0.5
# Set a seed for reproducibility
set.seed(141)
# Sample a single observation
pg::rpg_scalar(h, z)
#> [1] 0.05752942
# Set a seed for reproducibility
set.seed(141)
# Sample a vector of observations
pg::rpg_vector(n, h, z)
#> [,1]
#> [1,] 0.05752942
#> [2,] 0.38752679
#> [3,] 0.38710433
#> [4,] 0.18847913
See also
The following are useful resources regarding the Polya Gamma distribution.
BayesLogit
R package by Nicholas G. Polson, James G. Scott, and Jesse Windle. Provides the main C++ class samplers contained used by the pg
package.pgdraw
by Daniel F. Schmidt and Enes Makalic. This package construction relies heavily on free-floating functions and Rcpp
data structures.bayesCL
by Rok Cesnovar and Erik Strumbelj. This package boast a sampler that is 100x faster through offloading of the computation onto a GPU. Though, the package is not actively maintained.Python
has the pypolyagamma
package by Scott Linderman.Stan
lacks an implementation for the Polya Gamma distribution since it relies on joint proposals rather than full conditionals.James Balamuta leaning heavily on work done in BayesLogit
R package by Nicholas G. Polson, James G. Scott, and Jesse Windle.
pg
package
To ensure future development of the package, please cite pg
package if used during an analysis or simulation study. Citation information for the package may be acquired by using in R:
GPL (>= 3)
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