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View Code? Open in Web Editor NEWC implementation of ANC HIV prevalence likelihood described by Alkema, Raftery, Clark (2007)
C implementation of ANC HIV prevalence likelihood described by Alkema, Raftery, Clark (2007)
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/`
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