Retrieves and filters data from the ERVISS (European Respiratory Virus Surveillance Summary). This is a generic function that can retrieve any of the available data types.
Usage
get_erviss_data(
type = ERVISS_TYPES,
csv_file = NULL,
date_min,
date_max,
pathogen = "",
variant = "",
indicator = "",
age = "",
countries = "",
min_value = 0,
use_snapshot = FALSE,
snapshot_date = NULL
)Arguments
- type
Type of data. One of: "positivity", "variants", "ili_ari_rates", "sari_rates", "sari_positivity", "nonsentinel_severity", "nonsentinel_tests".
- csv_file
Path to a local CSV file or URL containing the ERVISS data. If NULL (default), data is fetched from the official ERVISS repository.
- date_min
Start date of the period (Date object)
- date_max
End date of the period (Date object)
- pathogen
Character vector of pathogen names to filter. Used for types: "positivity", "sari_positivity", "nonsentinel_severity", "nonsentinel_tests". Use "" (default) to include all pathogens.
- variant
Character vector of variant names to filter. Only used for type = "variants". Use "" (default) to include all variants.
- indicator
Character vector of indicators to filter. The available values depend on the data type. Use "" (default) to include all indicators.
- age
Character vector of age groups to filter. Used for types: "ili_ari_rates", "sari_rates", "sari_positivity", "nonsentinel_severity", "nonsentinel_tests". Use "" (default) to include all age groups.
- countries
Character vector of country names to filter. Use "" (default) to include all countries.
- min_value
Minimum value threshold (default: 0). Only used for type = "variants".
- use_snapshot
Logical. If TRUE, fetches a historical snapshot; if FALSE (default), fetches the latest data. Ignored if csv_file is provided.
- snapshot_date
Date of the snapshot to retrieve. Required if use_snapshot = TRUE and csv_file is NULL.
Examples
# \donttest{
# Get positivity data
data <- get_erviss_data(
type = "positivity",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
countries = "France"
)
# Get ILI consultation rates
data <- get_erviss_data(
type = "ili_ari_rates",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
indicator = "ILIconsultationrate",
age = "total"
)
# Get non-sentinel severity data
data <- get_erviss_data(
type = "nonsentinel_severity",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
indicator = "hospitaladmissions"
)
# }