AgePopDenom

What is AgePopDenom?

AgePopDenom is an R package designed to facilitate the generation of fine-scale, age-structured population denominators for public health decision-making and service delivery. By combining census and household survey data with a novel parameter-based geostatistical modeling approach, the package produces high-resolution (5km x 5km) population estimates disaggregated by age.

Installation

System Requirements

Before installing AgePopDenom, ensure your system meets the following requirements:

1. R version: >= 4.1.0
2. C++ compiler: C++17 compatible
3. TMB (Template Model Builder)

Platform-Specific Setup

Windows

1. Install Rtools (matches your R version):

# Check if Rtools is installed and properly configured
pkgbuild::has_build_tools()

If FALSE, download and install Rtools from: CRAN Rtools

2. After installation, add Rtools to the system PATH:

echo 'export PATH="C:/rtools43/usr/bin;C:/rtools43/mingw64/bin:$PATH"' >> ~/.Renviron

3. Restart R and verify the correct compiler setup:

Sys.getenv("PATH")

It should include C:/rtools43/usr/bin and C:/rtools43/mingw64/bin.

4. Ensure the correct compiler is available:

g++ --version

It should output GCC version 10 or later.

5. Set up the Makevars.win file to use the correct compiler:

mkdir -p ~/.R
nano ~/.R/Makevars.win

Add the following lines:

CXX14=C:/rtools43/mingw64/bin/g++
CXX17=C:/rtools43/mingw64/bin/g++
CXX20=C:/rtools43/mingw64/bin/g++

Save and exit (CTRL+X, then Y, then Enter).

macOS

1. Install Command Line Tools:

xcode-select --install

2. Alternatively, install gcc via Homebrew:

brew install gcc

3. Install LLVM via Homebrew:

brew install llvm

4. Set up compiler paths:

For Zsh (default on macOS):

echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> ~/.zshrc
echo 'export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"' >> ~/.zshrc
echo 'export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"' >> ~/.zshrc
source ~/.zshrc

For Bash:

echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> ~/.bashrc
echo 'export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"' >> ~/.bashrc
echo 'export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"' >> ~/.bashrc
source ~/.bashrc

5. Verify the correct compiler is now being used:

clang++ --version

It should output Homebrew Clang (e.g., Homebrew clang version XXXXX).

6. Configure R to use LLVM: Modify your ~/.R/Makevars file:

nano ~/.R/Makevars

Add the following lines:

CXX=/opt/homebrew/opt/llvm/bin/clang++
CXX11=/opt/homebrew/opt/llvm/bin/clang++
CXX14=/opt/homebrew/opt/llvm/bin/clang++
CXX17=/opt/homebrew/opt/llvm/bin/clang++
CXX20=/opt/homebrew/opt/llvm/bin/clang++

Save and exit (CTRL+X, then Y, then Enter).

Linux (Ubuntu/Debian)

1. Update your system and install necessary packages:

sudo apt-get update
sudo apt-get install build-essential libxml2-dev

2. Ensure you have GCC installed:

sudo apt-get install g++

3. Install Clang (optional, if required for TMB compilation):

sudo apt-get install clang

4. Verify compiler setup:

g++ --version
clang++ --version

Install and Compile TMB

Restart R and install TMB:

install.packages("TMB", type = "source")

AgePopDenom installation

Once the setup is complete, follow the instructions below to download AgePopDenom

Note: AgePopDenom is currently under development. Once it is available on CRAN, you will be able to install it using the following command:

# install.packages("AgePopDenom")

To get the development version from GitHub, use:

# install.packages("devtools")
devtools::install_github("truenomad/AgePopDenom")

Then load it in R:

library(AgePopDenom)

Core Functions

1. Initialize project structure:

init()

2. Download required data:

# Example for Kenya and Uganda
countries <- c("KEN", "UGA")

# Get DHS data
download_dhs_datasets(countries, 
                      email = "my_email@example.com",
                      project = "Population denominator project")

# Process DHS data
process_dhs_data()

# Download shapefiles
download_shapefile(countries)

# Download population rasters from worldpop
download_pop_rasters(countries)

# Extract urban extent raster
extract_afurextent()

3. Run full analysis:

run_full_workflow(countries)

Documentation

For detailed documentation and examples, visit our package website.

Support and Contributions

For support, bug reports, or feature requests, please contact:

• Mo Yusuf (Package Developer)
  Email: moyusuf@who.int
  Affiliation: World Health Organization Regional Office for Africa, P.O. Box 06, Cite du Djoue, Brazzaville, Congo

Alternatively, open an issue on the GitHub repository.

We welcome contributions from the community to improve AgePopDenom.