diseasystore: ECDC Respiratory Viruses Weekly

library(diseasystore)

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
)

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(RSQLite::SQLite())
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
#> [1] "iliari_rates"   "infection_type" "age_group"

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"))
#> # Source:   table<`dbplyr_DZDwW3AwH0`> [?? x 6]
#> # Database: sqlite 3.45.2 []
#>   key_location age_group infection_type  rate valid_from valid_until
#>   <chr>        <chr>     <chr>          <dbl>      <dbl>       <dbl>
#> 1 Austria      <NA>      ILI            2072.      19387       19394
#> 2 Austria      <NA>      ILI            2140.      19380       19387
#> 3 Austria      <NA>      ILI            2160.      19394       19401
#> 4 Austria      <NA>      ILI            2411.      19373       19380
#> 5 Austria      <NA>      ILI            2469.      19401       19408
#> # ℹ more rows