Download and Clean WHO POLIS Data • polished

polished retrieves and cleans poliovirus surveillance data from the WHO Polio Information System (POLIS). The downloader writes each table to a local cache as raw_*; the cleaning pipeline reads those files and writes polished_* tables, with optional surveillance indicators and data-quality checks.

Installation

Install the development version from GitHub with pak::pak("truenomad/polished"). Downloading requires a POLIS API key, read from the POLIS_API_KEY environment variable.

The workflow

library(polished)

# 1. Download — writes raw_afp, raw_es, ... to a local cache (resumable, parallel)
get_polis_data(tables = c("case", "environmental_sample"), polis_folder = "data/polis")

# 2. Clean the downloaded tables and write outputs and quality reports
run_pipeline_dir("data/polis", "data/processed")
#   -> polished_afp.*, polished_es.*, polished_virus.*  + checks_*.xlsx workbooks

To create the project directories, a .Rprofile that defines cfg, and starter scripts for downloading and processing data:

# scaffolds the whole pipeline project, then run 2a (download) and 2b (process)
init_polis_pipeline("my_project", regions = "EMRO")

# add renv = TRUE to pin package versions (renv::snapshot / restore) for collaborators
init_polis_pipeline("my_project", regions = "EMRO", renv = TRUE)

Key functions

Function	Purpose
`get_polis_data()`	Download POLIS tables to a local cache, with resumable batches, parallel year downloads and checks for missing records.
`run_pipeline()` / `run_pipeline_dir()`	Clean tables in memory or from `raw_*` files, with optional geography reconciliation and surveillance indicators.
`clean_afp()` · `clean_es()` · `clean_human_spec()` · `clean_sia()`	Standardise columns, parse dates, derive variables, reconcile geography and remove duplicate records for each stream.
`clean_virus()`	Combine poliovirus-positive records from cleaned AFP and environmental samples.
`clean_pop()`	Prepare country, province and district population denominators, with optional WorldPop reconciliation.
`impute_geo_from_epid()`	Fill missing administrative names and GUIDs using EPID matches, and record the source of each fill.
`calc_polio_indicators()`	Calculate surveillance indicators from cleaned tables, including NPAFP rate, stool adequacy and timeliness.
`checks_afp()` … `write_checks_excel()`	Check cleaned tables and export a summary and flagged records to Excel.
`init_polis_pipeline()`	Create data directories, a project configuration and starter download and processing scripts.
`init_polis_project()`	Create directories for raw data, processed outputs, validation reports, caches and logs.

See the vignettes and each function’s help page (e.g. ?get_polis_data) for usage and data-formatting requirements.

Citation

To cite polished in publications, run citation("polished") in R, or use:

Yusuf, Mohamed A. (2026). polished: Retrieve and Prepare GPEI POLIS Surveillance Data. R package version 0.3.0. https://doi.org/10.5281/zenodo.22998766

@Manual{polished,
  title  = {polished: Retrieve and Prepare GPEI POLIS Surveillance Data},
  author = {Mohamed A. Yusuf},
  year   = {2026},
  note   = {R package version 0.3.0},
  url    = {https://github.com/truenomad/polished},
  doi    = {10.5281/zenodo.22998766},
}

License

MIT © Mohamed A. Yusuf. See license for details. Issues and pull requests welcome at https://github.com/truenomad/polished.