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zika-data's Introduction

DOI

Zika Data Guide

This repository contains data — and pointers to data — related to the 2015–16 Zika virus outbreak. Please feel free to suggest additions and/or modifications.

This repository also contains archived PDFs and data extracted from the resources below.

Global Data

Zika Virus

Mosquitoes

Per the WHO, "Zika virus is transmitted to people through the bite of an infected mosquito from the Aedes genus, mainly Aedes aegypti in tropical regions. This is the same mosquito that transmits dengue, chikungunya and yellow fever."

  • The global compendium of Aedes aegypti and Ae. albopictus occurrence. Data, as CSV files, available here. Published 2015-07-07 in Nature Scientific Data.
    • "A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 [...] derived from peer-reviewed literature and unpublished studies including national entomological surveys and expert networks. [...] This is the first comprehensive global database of Ae. aegypti and Ae. albopictus occurrence, consisting of 19,930 and 22,137 geo-positioned occurrence records respectively."

Country-Specific Data

Brazil

Colombia

Dominican Republic

El Salvador

Guatemala

  • Guatemala's Ministry of Health is publishing Zika data on its website. (See "Salas situacionales" at the bottom of the page.)

Haiti

Mexico

United States

Additional Resources

Acknowledgements

Special thanks to Torsten Wurm, @benparkergit, @pushthings4ward, Matt Osborn, Daniel Chen, Daina Bouquin, @cdcepi, and @derektlo.

Suggestions or Questions?

Please file an issue or email [email protected].

For more open-source data, methodologies, analyses, guides, and tools from BuzzFeed News, see BuzzFeedNews/everything.

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zika-data's Issues

Standardize data.

Surprise! Applications lake KNIME and ArcGIS have no clue what a tab separated value file is. I would suggest converting it to CSV.

paho-who-cases-reported-2016-02-24.tsv

This can easily be done by renaming the file extension to .csv and using a find and replace tool in your favorite editor to replace \t with ,

Adding more colombia municipal data

Just noticed there was a parser for the Colombia PDFs.

I can't seem to figure out how to use them.
There are 3 more new reports I'd like to add, but I can't seem to get the pdf into stdin for the script to parse.

Should I be loading parse-colombia-municipal.py as a python module? or is there a specific way to run it via command line by passing it a pdf to parse?

Weird Texas totals from March 9-23

I'm pulling the same information from the CDC and came across the issue of the center saying Texas had 19 travel-associated cases on March 9, then 34 cases on March 16 and then down to 23 on March 23.

I asked the CDC about the arch, and they responded Texas had double counted. Myself and another reporter have asked the Texas Department of Health about this and what they reported to the CDC.

Thought I'd bring this up because 34 cases in Texas for March 16 does not seem correct.

Colombia municipal data count mismatch

Data parsed from Colombia's latest municipality-level PDF provides these totals:

  • Confirmados por laboratorio: 1,050
  • Confirmados por clínica: 17,115
  • Sospechosos: 2,132

But the sum of these columns from the data I've parsed provides these totals:

  • Confirmados por laboratorio: 1,049 (-1)
  • Confirmados por clínica: 17,112 (-3)
  • Sospechosos: 2,117 (-15)

Am I missing one/several municipalities? Are the official totals wrong? Do they include unlisted municipalities? I've scoured the two files, but can't find the source of the discrepancy. Any ideas?

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