This project is an implementation of a combined implementation of the EPP and
Spectrum models used for UNAIDS HIV estimates. The purpose of this is to
integrate the demographic structure of the Spectrum model into the EPP model
used for estimating epidemic trends from surveillance data.

The repository maintains an R implementation and C++ implementation of the
model. Currently the demographic projection model takes an initial pulse and  
time series for the force of infection (r parameter), and implements the
R-spline model based on code from Dan Hogan. 

Eventually this will be extended to include the R-trend and EPP classic models. 
And then it will be extended to incorporate more flexible models for age-
specific incidence and force of infection.


Country-level input parameter values are read from country Spectrum files
available from UNAIDS: http://apps.unaids.org/spectrum/
These can be read into R using: https://github.com/jeffeaton/read-epp-spectrum


Files  
-----

- analysis-functions.R: functions to summarizes the outputs of the Spectrum
  model.

R/: subdirectory containing the full R implementation of the model.
-- 

- spectrum.R: R version of spectrum demographic projection model, and call to C version.
- epp.R: Implementation of r-spline version of EPP model (approximately).
- likelihood.R: R implementation of the likelihood (incomplete).
- test-spectrum.R: file to test R and C version of Spectrum projection model.
- test-rmat.R: test age-specific force-of-infection model [!!! CURRENTLY BROKEN]

C++/: subdirectory for the C++ implementation of the model
----

- parameters.h: definition of model parameter structure.
- parameters.c: functions to allocate and free parameters.
- states.cpp: state space functions
- states.h: state space declaration
- model.cpp: model definition
- model.h: declares fnSpectrum()
- rlib.cpp: wrapper function to be loaded into R
- test.cpp: test C++ model [!!! CURRENTLY BROKEN]
- mvndstpack.h: header file for C call to multivariate normal cdf.
- mvndstpack.f: multivariate normal cdf, from http://www.math.wsu.edu/faculty/genz/software/software.html


src/: subdirectory for C code [presently contains EPP, evenutally move from C++ directory]
----
- epp.c: C implementation of r-spline EPP model.



TODO:

- Tidy and document everything.
- Choose either C or C++.
- Bundle into an R package.
- Add read-epp-spectrum as submodule.
- Do research.