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## this script can be used to run really large models easily in order to test limits in SuiteSparse, Matrix, TMB, and INLA
## it loads simulated data created over all africa and all years

#############################################
## setup the environment for singularity R ##
#############################################

## Set core_repo location and tmb_repo loc
core_repo <- sprintf('/share/code/geospatial/lbd_core/')
tmb_repo  <- sprintf('/home/j/temp/azimmer/suitesparse_overloader')

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/* ========================================================================== */
/* === Supernodal/cholmod_super_symbolic ==================================== */
/* ========================================================================== */

/* -----------------------------------------------------------------------------
 * CHOLMOD/Supernodal Module. Copyright (C) 2005-2006, Timothy A. Davis
 * The CHOLMOD/Supernodal Module is licensed under Version 2.0 of the GNU
 * General Public License.  See gpl.txt for a text of the license.
 * CHOLMOD is also available under other licenses; contact authors for details.
 * http://www.suitesparse.com

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/* ========================================================================== */
/* === Supernodal/cholmod_super_numeric ===================================== */
/* ========================================================================== */

/* -----------------------------------------------------------------------------
 * CHOLMOD/Supernodal Module.  Copyright (C) 2005-2006, Timothy A. Davis
 * The CHOLMOD/Supernodal Module is licensed under Version 2.0 of the GNU
 * General Public License.  See gpl.txt for a text of the license.
 * CHOLMOD is also available under other licenses; contact authors for details.
 * http://www.suitesparse.com

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#===============================================================================
# SuiteSparse_config.mk:  common configuration file for the SuiteSparse
#===============================================================================

# This file contains all configuration settings for all packages authored or
# co-authored by Tim Davis:
#
# Package Version       Description
# ------- -------       -----------
# AMD     1.2 or later  approximate minimum degree ordering

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## Makefile for downloading the source code and building
## a binary package of R-INLA
##
## Run 'make' with no arguments for usage instructions
##
## This Makefile has been tested under Ubuntu 17.10
##
## Requirements:
##   mercurial
##   A full gcc/g++/gfortran installation

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#include <TMB.hpp>
#include <Eigen/Sparse>
#include <vector>
using namespace density;
using Eigen::SparseMatrix;

// helper function to make sparse SPDE precision matrix
// Inputs:
//    logkappa: log(kappa) parameter value
//    logtau: log(tau) parameter value

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  //////////////////////////////////////////////////////////////// 
  // Author: Nafis Sadat
  // Purpose: Forecasting model base across countries, incorporating ARIMA components
  // Created: Sometime in 2017
  ////////////////////////////////////////////////////////////////
  
  #include <TMB.hpp>
  #include <Eigen/Sparse>
  #include <vector>

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    require(ncdf4)  
    require(ncdf4.helpers)
    require(data.table)
    
    ## Get the name of the value vars in the nc file
    get_nc_value_name <- function(nc_file) {
      
      ## Get names
      nc_obj <- nc_open(nc_file)
      name<-names(nc_obj$var)

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## Makefile for downloading the source code and building
## a binary package of R-INLA on Debian/Buster
## using a custom version of R and Intel MKL
## Intended for use by : Institute for Health Metrics and Evaulation
##
## Maintained by : Nafis Sadat, [email protected]
##
## Run 'make' with no arguments for usage instructions
##
## This Makefile has been tested under Debian GNU/Linux