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This implements the random effects likelihood for ANC HIV prevalence described by
Alkema, Raftery, Clark Ann Appl Stat 2007 (http://dx.doi.org/10.1214/07-AOAS111).
This is implemented in the EPP model used by UNAIDS for generating HIV epidemic
trends: http://www.unaids.org/en/dataanalysis/datatools/spectrumepp2013.

The code is implemeted as an R package in the subdirectory anclik/. To install the
R package using devtools:

> devtools::install_github("jeffeaton/anclik")


The script "R/anclik.R" includes a function for preparing ANC data for likelihood
calculation and a wrapper function for calling the C function. This includes
an equivalent R implementation of the C code.

The script "example.R" provides an example for preparing the data and
calling the likelihood, and compares the performance of the C and R
implementations.


The initial implementation relied on GNU Scientific Library (GSL) for
adapative Gaussian quadrature numerical intergration routine
(http://www.gnu.org/software/gsl/). This deprecated version is retained in
"gsl/anclikR_gsl.c". To compile that version add the flags -lgsl -lgslcblas:

$ R CMD SHLIB -lgsl -lgslcblas anclikR_gsl.c anclik.c mvrandist.c

You may need to supply -L <path to GSL> if not in the PATH variable.

At present, it does not handle the GSL errors, so in this version if an error
happens in the C code (e.g. pass it a vector of incorrect size), it will crash R.
Hopefully I’ll improve this in the future. 


GPLv3, no warranty, etc...

Created by Jeff Eaton on 2014-11-12 <[email protected]>
Edited by  Jeff Eaton on 2014-11-24
Edited by  Jeff Eaton on 2016-05-29: Remove dependency on GSL
Edited by  Jeff Eaton on 2022-02-23: Move R package to top level, GSL version to `gsl/`