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Process Weekly Cholera Data from JHU: Convert to MOSAIC Format

Source: R/process_JHU_data.R
process_JHU_weekly_data.Rd

This function processes raw weekly cholera surveillance data from the JHU Public Surveillance Dataset, aggregates to country level, parses ISO-weeks, computes week start/end dates, and prepares the data for the MOSAIC framework.

Usage

process_JHU_weekly_data(PATHS)

Arguments

PATHS

A list containing paths to the raw and processed data directories. Should include:

  • DATA_RAW: Path to the directory containing Public_surveillance_dataset.rds.

  • DATA_JHU_WEEKLY: Path to save the processed cholera data (e.g., cholera_country_weekly_processed.csv).

Value

Invisibly returns NULL. Side effects:

  • Reads raw data with readRDS().

  • Writes processed data to PATHS$DATA_JHU_WEEKLY/cholera_country_weekly_processed.csv via write.csv().

Details

Steps performed:

  • Load Public_surveillance_dataset.rds and keep only spatial_scale == "country".

  • Drop rows flagged phantom: weeks the archive zero-fills without a report (no observation_collection_id). They are unobserved, not zeros.

  • Extract iso_code from location_name (suffix after “::”) and convert to full country name.

  • Split epiweek (e.g. "2017-15") into year and week.

  • Create date_start (Monday) and date_stop (Sunday) for each ISO week via ISOweek::ISOweek2date().

  • Compute month from date_start using lubridate::month().

  • Define cases using suspected (sCh) if present, else confirmed (cCh), else NA.

  • Keep deaths as reported; a missing death count stays NA (it is not an observed zero – about three quarters of country-level rows in the OSF archive carry no death count).

  • Drop rows where both cases and deaths are NA (no observation).

  • Save a data.frame with columns: country, iso_code, year, month, week, date_start, date_stop, cases, deaths.

Examples

if (FALSE) { # \dontrun{
PATHS <- list(
  DATA_RAW        = "data/raw",
  DATA_JHU_WEEKLY = "data/processed/jhu_weekly"
)
process_JHU_weekly_data(PATHS)
} # }