diseasystore: ECDC Respiratory Viruses Weekly"

In diseasystore: Feature Stores for the 'diseasy' Framework

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(diseasystore)

if (rlang::is_installed("withr")) {
  withr::local_options(
    "tibble.print_min" = 5,
    "diseasystore.verbose" = FALSE,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE
  )
} else {
  opts <- options(
    "tibble.print_min" = 5,
    "diseasystore.verbose" = FALSE,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE
  )
}

# We have a "hard" dependency for duckdb to render parts of this vignette
suggests_available <- rlang::is_installed("duckdb")
not_on_cran <- interactive() || identical(Sys.getenv("NOT_CRAN"), "true") ||
  identical(Sys.getenv("CI"), "true")

The Respiratory viruses weekly repository contains weekly summaries of the erviss data for Influenza-Like Illness (ILI) and Acute Respiratory Infection (ARI).

This vignette shows how to use (some of) this data through the diseasystore package.

First, it is a good idea to clone the repository locally and store that location as an option for the package.

# First we set the path we want to use as an option
options(
  "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" =
    file.path("local", "path")
)

# Ensure folder exists
source_conn <- diseasyoption("source_conn", "DiseasystoreEcdcRespiratoryViruses")
if (!dir.exists(source_conn)) {
  dir.create(source_conn, recursive = TRUE, showWarnings = FALSE)
}

# Clone the repository
system2(
  "git",
  args = c(
    paste("-C", source_conn),
    "clone https://github.com/EU-ECDC/Respiratory_viruses_weekly_data"
  ),
  stdout = TRUE
)

# In practice, it is best to make a local copy of the data which is
# stored in the "vignette_data" folder.
# This folder can either be in the package folder
# (preferred, please create the folder) or in the tempdir().
local_conn <- purrr::detect(
  "vignette_data",
  checkmate::test_directory_exists,
  .default = tempdir()
)

if (rlang::is_installed("withr")) {
  withr::local_options(
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" = local_conn,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.n_max" = 1000
  )
} else {
  opts <- c(
    opts,
    options(
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" = local_conn,
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.n_max" = 1000
    )
  )
}

# Define the ECDC file to download
test_file <- "data/snapshots/2023-11-24_ILIARIRates.csv"

# Create folder and download file
dir.create(
  dirname(file.path(local_conn, test_file)),
  recursive = TRUE,
  showWarnings = FALSE
)

if (!file.exists(file.path(local_conn, test_file))) {
  remote_file <- source_conn_github(
    diseasyoption("remote_conn", "DiseasystoreEcdcRespiratoryViruses"),
    test_file
  )

  readr::read_csv(
    remote_file,
    n_max = 1000,
    show_col_types = FALSE,
    progress = FALSE
  ) |>
    readr::write_csv(file.path(local_conn, test_file))
}

# Check that the files are available after attempting to download
files_missing <- purrr::some(
  test_file,
  ~ !checkmate::test_file_exists(file.path(local_conn, .))
)
if (files_missing) {
  data_available <- FALSE
} else {
  data_available <- TRUE
}

The diseasystores require a database to store its features in. These should be configured before use and can be stored in the packages options.

# We define target_conn as a function that opens a DBIconnection to the DB
target_conn <- \() DBI::dbConnect(duckdb::duckdb())
options(
  "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
)

target_conn <- \() DBI::dbConnect(duckdb::duckdb())
if (rlang::is_installed("withr")) {
  withr::local_options(
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
  )
} else {
  opts <- c(
    opts,
    options(
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
    )
  )
}

Once the files are downloaded and the target database is configured, we can initialize the diseasystore that uses the ECDC Respiratory Viruses Weekly data.

ds <- DiseasystoreEcdcRespiratoryViruses$new()

Once configured such, we can use the feature store directly to get data.

# We can see all the available features in the feature store
ds$available_features

If you have locally cloned the repository, you may consider pulling data from the repository manually and disabling automatic pulls. Otherwise, the diseasystore will check for updates every time you request a feature.

# Manually update the repository
system2(
  "git",
  args = paste(
    "-C",
    diseasyoption("source_conn", "DiseasystoreEcdcRespiratoryViruses")
  ),
  stdout = TRUE
)

# Disable automatic pulls
options("diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE)

# And then retrieve a feature from the feature store
ds$get_feature(
  feature = "iliari_rates",
  start_date = as.Date("2023-01-01"),
  end_date = as.Date("2023-03-01")
)

if (exists("ds")) rm(ds)
gc()
if (!rlang::is_installed("withr")) {
  options(opts)
}

diseasystore documentation built on April 4, 2025, 5:56 a.m.