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_*; an end-to-end pipeline then reads those raw_* inputs and writes
cleaned, analysis-ready polished_* tables, with optional surveillance
indicators and data-quality checks.
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.
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 + indicators + checks in one call: raw_* in, polished_* out
run_pipeline_dir("data/polis", "data/processed")
# -> polished_afp.*, polished_es.*, polished_virus.* + checks_*.xlsx workbooksFor a complete, reproducible project — the 01_data domain layout, a wired
.Rprofile (the cfg manifest), and runnable download + process scripts — in
one call:
# 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)| Function | Purpose |
|---|---|
get_polis_data() |
Pull one or many POLIS tables into a local cache. Works around POLIS's year-aligned date filters and Id-range pagination, checkpoints each batch so an interrupted pull resumes cleanly, fetches years in parallel, and verifies completeness against POLIS. |
run_pipeline() / run_pipeline_dir() |
Run the whole cleaning set — AFP, ES, human specimens, SIA, and the derived virus positives — in memory or from a directory of raw_* files, with optional admin reconciliation and surveillance indicators. |
clean_afp() · clean_es() · clean_human_spec() · clean_sia() · clean_virus() |
The per-stream cleaners: standardise names, sanitise dates, derive analytic variables, reconcile geography, dedup to one row per POLIS id. |
clean_pop() |
Clean the POLIS population reference into adm0/adm1/adm2 under-5 / under-15 / all-ages denominators, optionally reconciled against WorldPop and rolled up by boundary validity; the rate-indicator base. |
impute_geo_from_epid() |
Recover missing administrative geography from the EPID through an ordered, provenance-stamped cascade — fills only blank cells, never fabricates on ambiguity. |
calc_polio_indicators() |
Compute the WHO POLIS indicator catalogue (NPAFP rate, stool adequacy, timeliness, dose, ES, virus, SIA, composite families) from the cleaned tables. |
checks_afp() … write_checks_excel() |
Per-stream data-quality checks exported as a styled Excel workbook, one tab per check. |
init_polis_pipeline() |
Scaffold a full pipeline project in one call — the 01_data domain layout, a wired .Rprofile (the cfg manifest), a .gitignore, and runnable download / process scripts. |
init_polis_project() |
Set up a lighter raw / processed / cache project workspace and stream the pipeline into it. |
See the vignettes and each function's
help page (e.g. ?get_polis_data) for usage and data-formatting requirements.
To cite polished in publications, run citation("polished") in R, or use:
Yusuf, Mohamed A. (2026). polished: Download and Clean WHO POLIS Data. R package version 0.1.0. https://github.com/truenomad/polished
@Manual{polished,
title = {polished: Download and Clean WHO POLIS Data},
author = {Mohamed A. Yusuf},
year = {2026},
note = {R package version 0.1.0},
url = {https://github.com/truenomad/polished},
}
MIT © Mohamed A. Yusuf. See LICENSE for details. Issues and pull requests welcome at https://github.com/truenomad/polished.