Dengue incidence address geocoding in HCMC

This repo is part of the "Spatiotemporal modelling of dengue incidence in HCMC" project, funded by OUCRU-PSC.

The project proposed duration is Dec 2025 - Nov 2026

Dependencies

This project uses OUCRU-Modelling/tidygeocoder, a fork of the tidygeocoder R package that implements Vietmap's geocoding API.

Navigating the repo

dengue-geocoding/
├── R/            Helper functions
├── codes/        Data cleaning and exporting workflow
├── data/         Input and output data
├── geocoding/    Script for geocoding
└── notebooks/    .Rmd files for visualizing incidence data

Data cleaning and exporting (codes/)

Main workflow:

• 01_clean_incidence_data.R clean and standardize raw incidence data

• 02_generate_to_geocode.R and 02_generate_to_geocode_bd_vt.R: extract unique addresses for geocoding

  • Output:

    • data/cached/to_geocode_df.qs HCMC data before 2025 merge

    • data/cached/to_geocode_bd_vt_df.qs Binh Duong, Vung Tau data before 2025 merge

  • The geocoding process is handled separately

• 04_export_geocoded_*.R export incidence data with the GPS coordinates

• 05_generate_to_geocode_aug2025.R extracting addresses (after 2025 merge) for geocoding, also checks against existing geocoded results to avoid duplicate geocoding.

• 06_export_geocoded_aug2025.R export post-reform incidence data with the GPS coordinates

• 07_export_data_w_sf.R export data bundle (.rds) with incidence data and lookup table for shapefiles

• 08_postreform_by_mapping.R update post-reform commune when pre-reform was not splitted during merge

• 99_*.R miscellaneous posthoc checks

Data geocoding (geocoding/)

Main scripts:

• main.R script for geocoding addresses using VietMap API

  • Input: data/cached/to_geocoded_df.qs

  • Output:

    • data/cached/geocoded_addr.qs successfully geocoded addresses

    • data/cached/failed_geocoded_addr.qs addresses that failed geocoding

• geocode_script.sh bash script to dispatch the geocoding script on OUCRU's HPC