flusight-csv-tools

flusight-csv-tools

Node toolkit for CDC FluSight format CSVs. Full documentation here. Provides features for:

• Parsing CSVs (fct.Csv class)
• Verifying CSVs (fct.verify module)
• Scoring targets (fct.score module)
• Fetching true values (fct.truth module)
• Metadata related to CDC FluSight (fct.meta module)
• Utilities for working with
  • Bin distributions (fct.utils.bins module)
  • Time and epiweeks (fct.utils.epiweek module)

Quickstart

# Install from npm
npm i flusight-csv-tools

// Read a csv
const fct = require('flusight-csv-tools')
let csv = new fct.Csv('./test/data/sample.csv', 201720, 'model-name')

// Verify
fct.verify.verifyHeaders(csv)
fct.verify.verifyPoint(csv)
fct.verify.verifyProbabilities(csv)

// Score
fct.score.score(csv).then(d => ...)

Data representation

A CSV ingested by flusight-csv-tools uses the following standards for representing information:

• HHS Regions are referred to as nat (for 'US National') or hhs1, hhs2... for 'HHS Region 1', 'HHS Region 2' and so on.
• Week ahead targets are referred using 1-ahead, 2-ahead, 3-ahead and 4-ahead while seasonal targets are peak (peak wili value), peak-wk and onset-wk.
• A season 20xx-20yy is represented using a single number 20xx (the first year of a season).
• Weeks values are not represented by themselves but are always passed around as epiweeks like YYYYWW where YYYY is the year and WW is the week (MMWR week).
• An epidemic season 20xx contains all weeks in the set [20xx30, 20yy29], where 20yy = 20xx + 1.
• CSVs are scored using the latest available data and do not, as of yet, use the data available at the time the predictions were made.