| Title: | Retrieve and Explore ERVISS Respiratory Virus Surveillance Data |
| Version: | 0.1.0 |
| Description: | Provides easy access to ERVISS (European Respiratory Virus Surveillance Summary) data from the EU-ECDC https://github.com/EU-ECDC/Respiratory_viruses_weekly_data. Enables retrieval, filtering, and optional visualization of data across European countries. Data is fetched directly from the EU-ECDC Respiratory Viruses Weekly Data repository, with support for both latest data and historical snapshots for reproducible analyses. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/Epiconcept-Paris/ervissexplore, https://epiconcept-paris.github.io/ervissexplore/ |
| BugReports: | https://github.com/Epiconcept-Paris/ervissexplore/issues |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| Imports: | cli, data.table, ggplot2 |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2026-02-16 08:58:47 UTC; Yohann Mansiaux |
| Author: | Yohann Mansiaux [aut, cre] |
| Maintainer: | Yohann Mansiaux <y.mansiaux@epiconcept.fr> |
| Repository: | CRAN |
| Date/Publication: | 2026-02-19 19:50:08 UTC |
Get ERVISS data
Description
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. |
Value
A data.table containing the filtered data.
Examples
# 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"
)
Get ERVISS data URL
Description
Builds the URL to download ERVISS data, either the latest batch or a specific snapshot.
Usage
get_erviss_url(type = ERVISS_TYPES, 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". |
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest positivity data URL
get_erviss_url("positivity")
# Get latest variants data URL
get_erviss_url("variants")
# Get latest ILI/ARI rates data URL
get_erviss_url("ili_ari_rates")
# Get snapshot URL
get_erviss_url("variants", use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS variants data
Description
Retrieves and filters SARS-CoV-2 variant data from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, variant(s), and country(ies).
Usage
get_erviss_variants(
csv_file = NULL,
date_min,
date_max,
variant = "",
countries = "",
min_value = 0,
indicator = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
variant |
Character vector of variant names to filter. Use "" (default) to include all variants. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
min_value |
Minimum value threshold to include in the results (default: 0) |
indicator |
Type of indicator: "proportion" or "detections". Use "" (default) to include all indicators. |
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. |
Value
A data.table containing the filtered variant data with columns: date, value, variant, countryname, indicator, and other ERVISS fields.
Examples
# Get latest variant data for France
data <- get_erviss_variants(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
countries = "France"
)
# Get specific variants with minimum proportion threshold
data <- get_erviss_variants(
date_min = as.Date("2024-06-01"),
date_max = as.Date("2024-12-31"),
variant = c("XFG", "LP.8.1"),
min_value = 5
)
Get ERVISS variants data URL
Description
Builds the URL to download ERVISS variants data, either the latest batch or a specific snapshot.
Usage
get_erviss_variants_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_erviss_variants_url()
# Get snapshot URL
get_erviss_variants_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS ILI/ARI consultation rates data
Description
Retrieves and filters ILI (Influenza-Like Illness) and ARI (Acute Respiratory Infection) consultation rates from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, indicator(s), age group(s), and country(ies).
Usage
get_ili_ari_rates(
csv_file = NULL,
date_min,
date_max,
indicator = "",
age = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
indicator |
Character vector of indicators to filter: "ILIconsultationrate", "ARIconsultationrate", or both. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered ILI/ARI rates data with columns: survtype, countryname, date, indicator, age, value.
Examples
# Get ILI consultation rates for France
data <- get_ili_ari_rates(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
indicator = "ILIconsultationrate",
countries = "France"
)
# Get both ILI and ARI rates for all countries
data <- get_ili_ari_rates(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31")
)
Get ERVISS ILI/ARI rates data URL
Description
Builds the URL to download ERVISS ILI/ARI consultation rates data, either the latest batch or a specific snapshot.
Usage
get_ili_ari_rates_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_ili_ari_rates_url()
# Get snapshot URL
get_ili_ari_rates_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS non-sentinel severity data
Description
Retrieves and filters non-sentinel severity data (deaths, hospital admissions, ICU admissions, etc.) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), age group(s), and country(ies).
Usage
get_nonsentinel_severity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "deaths", "hospitaladmissions", "ICUadmissions", "ICUinpatients", "hospitalinpatients", or any combination. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered severity data with columns: survtype, countryname, date, pathogen, pathogentype, indicator, age, value.
Examples
# Get hospital admissions for SARS-CoV-2 in France
data <- get_nonsentinel_severity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
indicator = "hospitaladmissions",
countries = "France"
)
# Get all severity indicators
data <- get_nonsentinel_severity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2"
)
Get ERVISS non-sentinel severity data URL
Description
Builds the URL to download ERVISS non-sentinel severity data, either the latest batch or a specific snapshot.
Usage
get_nonsentinel_severity_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_nonsentinel_severity_url()
# Get snapshot URL
get_nonsentinel_severity_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS non-sentinel tests/detections data
Description
Retrieves and filters non-sentinel virological testing data (tests and detections) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), age group(s), and country(ies).
Usage
get_nonsentinel_tests(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "detections", "tests", or both. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered non-sentinel tests data with columns: survtype, countryname, date, pathogen, pathogentype, pathogensubtype, indicator, age, value.
Examples
# Get non-sentinel detections for Influenza in France
data <- get_nonsentinel_tests(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = "detections",
countries = "France"
)
# Get all non-sentinel test data
data <- get_nonsentinel_tests(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31")
)
Get ERVISS non-sentinel tests/detections data URL
Description
Builds the URL to download ERVISS non-sentinel tests/detections data, either the latest batch or a specific snapshot.
Usage
get_nonsentinel_tests_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_nonsentinel_tests_url()
# Get snapshot URL
get_nonsentinel_tests_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS SARI tests/detections/positivity data
Description
Retrieves and filters SARI (Severe Acute Respiratory Infection) virological data (tests, detections, positivity) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), age group(s), and country(ies).
Usage
get_sari_positivity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "positivity", "detections", "tests", or any combination. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "total", "0-4", "5-14", "15-64", "65+"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered SARI data with columns: survtype, countryname, date, pathogen, pathogentype, pathogensubtype, indicator, age, value.
Examples
# Get SARI positivity data for Influenza in France
data <- get_sari_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = "positivity",
countries = "France"
)
# Get all SARI indicators for SARS-CoV-2
data <- get_sari_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2"
)
Get ERVISS SARI tests/detections/positivity data URL
Description
Builds the URL to download ERVISS SARI virological data, either the latest batch or a specific snapshot.
Usage
get_sari_positivity_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_sari_positivity_url()
# Get snapshot URL
get_sari_positivity_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS SARI rates data
Description
Retrieves and filters SARI (Severe Acute Respiratory Infection) rates from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, age group(s), and country(ies).
Usage
get_sari_rates(
csv_file = NULL,
date_min,
date_max,
age = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered SARI rates data with columns: survtype, countryname, date, indicator, age, value.
Examples
# Get SARI rates for Spain
data <- get_sari_rates(
date_min = as.Date("2025-01-01"),
date_max = as.Date("2025-12-31"),
countries = "Spain"
)
# Get SARI rates for specific age groups
data <- get_sari_rates(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
age = c("0-4", "65+")
)
Get ERVISS SARI rates data URL
Description
Builds the URL to download ERVISS SARI rates data, either the latest batch or a specific snapshot.
Usage
get_sari_rates_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_sari_rates_url()
# Get snapshot URL
get_sari_rates_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Get ERVISS sentinel tests data
Description
Retrieves and filters sentinel surveillance data (positivity, detections, tests) from the ERVISS (European Respiratory Virus Surveillance Summary) for a specified date range, pathogen(s), indicator(s), and country(ies).
Usage
get_sentineltests_positivity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
countries = "",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "positivity", "detections", "tests", or any combination. Use "" (default) to include all indicators. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
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. |
Value
A data.table containing the filtered data with columns: date, value, pathogen, countryname, indicator, and other ERVISS fields.
Examples
# Get latest SARS-CoV-2 positivity data for France
data <- get_sentineltests_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
countries = "France"
)
# Get detections and tests
data <- get_sentineltests_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = c("detections", "tests")
)
# Get historical data from a specific snapshot
data <- get_sentineltests_positivity(
date_min = as.Date("2023-01-01"),
date_max = as.Date("2023-12-31"),
use_snapshot = TRUE,
snapshot_date = as.Date("2024-02-23")
)
Get ERVISS positivity data URL
Description
Builds the URL to download ERVISS positivity data, either the latest batch or a specific snapshot.
Usage
get_sentineltests_positivity_url(use_snapshot = FALSE, snapshot_date = NULL)
Arguments
use_snapshot |
Logical. If TRUE, returns a snapshot URL; if FALSE (default), returns the URL for the latest data. |
snapshot_date |
Date of the snapshot to retrieve (required if use_snapshot = TRUE). Must be a Date object. |
Value
A character string containing the URL
Examples
# Get latest data URL
get_sentineltests_positivity_url()
# Get snapshot URL
get_sentineltests_positivity_url(use_snapshot = TRUE, snapshot_date = as.Date("2023-11-24"))
Plot ERVISS data
Description
Creates a ggplot2 visualization of ERVISS data, with facets by country. This is a generic function that can plot any of the available data types.
Usage
plot_erviss_data(
data,
type = ERVISS_TYPES,
date_breaks = NULL,
date_format = "%b %Y"
)
Arguments
data |
A data.table or data.frame containing ERVISS data, typically output from
|
type |
Type of data. One of: "positivity", "variants", "ili_ari_rates", "sari_rates", "sari_positivity", "nonsentinel_severity", "nonsentinel_tests". |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks"). If NULL, a sensible default is chosen based on the data type. |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
# Plot positivity data
data <- get_erviss_data("positivity",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
pathogen = "SARS-CoV-2"
)
plot_erviss_data(data, type = "positivity")
# Plot ILI/ARI rates
data <- get_erviss_data("ili_ari_rates",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
indicator = "ILIconsultationrate"
)
plot_erviss_data(data, type = "ili_ari_rates")
Plot ERVISS positivity data
Description
Creates a ggplot2 visualization of positivity data, with facets by country and colored by pathogen. The plot title displays mean, min and max positivity values.
Usage
plot_erviss_positivity(data, date_breaks = "2 weeks", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing positivity data, typically output from
|
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_sentineltests_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
pathogen = "SARS-CoV-2"
)
plot_erviss_positivity(data, date_breaks = "1 month")
Plot ERVISS variants data
Description
Creates a ggplot2 visualization of variant data, with facets by country and colored by variant. The y-axis shows percentage of all variants.
Usage
plot_erviss_variants(data, date_breaks = "1 month", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing variant data, typically output from
|
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_erviss_variants(
date_min = as.Date("2024-06-01"),
date_max = as.Date("2024-12-31"),
variant = c("XFG", "LP.8.1")
)
plot_erviss_variants(data, date_breaks = "1 month")
Plot ERVISS ILI/ARI consultation rates data
Description
Creates a ggplot2 visualization of ILI/ARI consultation rates, with facets by country and colored by age group.
Usage
plot_ili_ari_rates(data, date_breaks = "2 weeks", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing ILI/ARI rates data, typically
output from |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_ili_ari_rates(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
indicator = "ILIconsultationrate"
)
plot_ili_ari_rates(data, date_breaks = "1 month")
Plot ERVISS non-sentinel severity data
Description
Creates a ggplot2 visualization of non-sentinel severity data, with facets by country and colored by pathogen.
Usage
plot_nonsentinel_severity(
data,
date_breaks = "1 month",
date_format = "%b %Y"
)
Arguments
data |
A data.table or data.frame containing severity data, typically
output from |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_nonsentinel_severity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
pathogen = "SARS-CoV-2",
indicator = "hospitaladmissions"
)
plot_nonsentinel_severity(data, date_breaks = "1 month")
Plot ERVISS non-sentinel tests/detections data
Description
Creates a ggplot2 visualization of non-sentinel tests/detections data, with facets by country and colored by pathogen.
Usage
plot_nonsentinel_tests(data, date_breaks = "1 month", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing non-sentinel tests data,
typically output from |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_nonsentinel_tests(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
pathogen = "Influenza",
indicator = "detections"
)
plot_nonsentinel_tests(data, date_breaks = "1 month")
Plot ERVISS SARI positivity data
Description
Creates a ggplot2 visualization of SARI positivity data, with facets by country and colored by pathogen.
Usage
plot_sari_positivity(data, date_breaks = "2 weeks", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing SARI positivity data, typically
output from |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_sari_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-06-30"),
pathogen = "Influenza",
indicator = "positivity"
)
plot_sari_positivity(data, date_breaks = "1 month")
Plot ERVISS SARI rates data
Description
Creates a ggplot2 visualization of SARI rates, with facets by country and colored by age group.
Usage
plot_sari_rates(data, date_breaks = "2 weeks", date_format = "%b %Y")
Arguments
data |
A data.table or data.frame containing SARI rates data, typically
output from |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
Value
A ggplot2 object
Examples
data <- get_sari_rates(
date_min = as.Date("2025-01-01"),
date_max = as.Date("2025-06-30"),
countries = "Spain"
)
plot_sari_rates(data, date_breaks = "1 month")
Quick plot of ERVISS data
Description
Convenience function that fetches and plots ERVISS data in one step.
This is a generic function that can handle any of the available data types.
For more control, use get_erviss_data followed by
plot_erviss_data.
Usage
quick_plot_erviss_data(
type = ERVISS_TYPES,
csv_file = NULL,
date_min,
date_max,
pathogen = "",
variant = "",
indicator = "",
age = "",
countries = "",
min_value = 0,
date_breaks = NULL,
date_format = "%b %Y",
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". |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks"). If NULL, a sensible default is chosen based on the data type. |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing the data over time by country
Examples
# Quick visualization of positivity data
quick_plot_erviss_data(
type = "positivity",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2"
)
# Quick visualization of ILI rates
quick_plot_erviss_data(
type = "ili_ari_rates",
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
indicator = "ILIconsultationrate"
)
Quick plot of ERVISS positivity data
Description
Convenience function that fetches and plots ERVISS positivity data in one step.
For more control, use get_sentineltests_positivity followed by
plot_erviss_positivity.
Usage
quick_plot_erviss_positivity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
countries = "",
date_breaks = "2 weeks",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "positivity", "detections", "tests", or any combination. Use "" (default) to include all indicators. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing positivity over time by country and pathogen
Examples
# Quick visualization of latest data
quick_plot_erviss_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
date_breaks = "1 month"
)
Quick plot of ERVISS variants data
Description
Convenience function that fetches and plots ERVISS variant data in one step.
For more control, use get_erviss_variants followed by
plot_erviss_variants.
Usage
quick_plot_erviss_variants(
csv_file = NULL,
date_min,
date_max,
variant = "",
countries = "",
min_value = 0,
indicator = "",
date_breaks = "1 month",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
variant |
Character vector of variant names to filter. Use "" (default) to include all variants. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
min_value |
Minimum value threshold to include in the results (default: 0) |
indicator |
Type of indicator: "proportion" or "detections". Use "" (default) to include all indicators. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing variant proportions over time by country
Examples
# Quick visualization of latest variant data
quick_plot_erviss_variants(
date_min = as.Date("2024-06-01"),
date_max = as.Date("2024-12-31"),
variant = c("XFG", "LP.8.1"),
date_breaks = "1 month"
)
Quick plot of ERVISS ILI/ARI consultation rates data
Description
Convenience function that fetches and plots ERVISS ILI/ARI consultation rates
data in one step.
For more control, use get_ili_ari_rates followed by
plot_ili_ari_rates.
Usage
quick_plot_ili_ari_rates(
csv_file = NULL,
date_min,
date_max,
indicator = "",
age = "",
countries = "",
date_breaks = "2 weeks",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
indicator |
Character vector of indicators to filter: "ILIconsultationrate", "ARIconsultationrate", or both. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing ILI/ARI consultation rates over time by country and age group
Examples
# Quick visualization of ILI rates
quick_plot_ili_ari_rates(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
indicator = "ILIconsultationrate",
date_breaks = "1 month"
)
Quick plot of ERVISS non-sentinel severity data
Description
Convenience function that fetches and plots ERVISS non-sentinel severity
data in one step.
For more control, use get_nonsentinel_severity followed by
plot_nonsentinel_severity.
Usage
quick_plot_nonsentinel_severity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
date_breaks = "1 month",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "deaths", "hospitaladmissions", "ICUadmissions", "ICUinpatients", "hospitalinpatients", or any combination. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing severity data over time by country and pathogen
Examples
# Quick visualization of hospital admissions
quick_plot_nonsentinel_severity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "SARS-CoV-2",
indicator = "hospitaladmissions",
date_breaks = "1 month"
)
Quick plot of ERVISS non-sentinel tests/detections data
Description
Convenience function that fetches and plots ERVISS non-sentinel tests/detections
data in one step.
For more control, use get_nonsentinel_tests followed by
plot_nonsentinel_tests.
Usage
quick_plot_nonsentinel_tests(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
date_breaks = "1 month",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "detections", "tests", or both. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing non-sentinel tests/detections over time by country and pathogen
Examples
# Quick visualization of non-sentinel detections
quick_plot_nonsentinel_tests(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = "detections",
date_breaks = "1 month"
)
Quick plot of ERVISS SARI positivity data
Description
Convenience function that fetches and plots ERVISS SARI positivity data
in one step.
For more control, use get_sari_positivity followed by
plot_sari_positivity.
Usage
quick_plot_sari_positivity(
csv_file = NULL,
date_min,
date_max,
pathogen = "",
indicator = "",
age = "",
countries = "",
date_breaks = "2 weeks",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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. Use "" (default) to include all pathogens. |
indicator |
Character vector of indicators to filter: "positivity", "detections", "tests", or any combination. Use "" (default) to include all indicators. |
age |
Character vector of age groups to filter (e.g., "total", "0-4", "5-14", "15-64", "65+"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing SARI positivity over time by country and pathogen
Examples
# Quick visualization of SARI positivity
quick_plot_sari_positivity(
date_min = as.Date("2024-01-01"),
date_max = as.Date("2024-12-31"),
pathogen = "Influenza",
indicator = "positivity",
date_breaks = "1 month"
)
Quick plot of ERVISS SARI rates data
Description
Convenience function that fetches and plots ERVISS SARI rates data in one step.
For more control, use get_sari_rates followed by
plot_sari_rates.
Usage
quick_plot_sari_rates(
csv_file = NULL,
date_min,
date_max,
age = "",
countries = "",
date_breaks = "2 weeks",
date_format = "%b %Y",
use_snapshot = FALSE,
snapshot_date = NULL
)
Arguments
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) |
age |
Character vector of age groups to filter (e.g., "0-4", "5-14", "15-64", "65+", "total"). Use "" (default) to include all age groups. |
countries |
Character vector of country names to filter. Use "" (default) to include all countries. |
date_breaks |
A string specifying the date breaks for the x-axis (e.g., "1 month", "2 weeks") |
date_format |
A string specifying the date format for x-axis labels
(e.g., |
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. |
Value
A ggplot2 object showing SARI rates over time by country and age group
Examples
# Quick visualization of SARI rates
quick_plot_sari_rates(
date_min = as.Date("2025-01-01"),
date_max = as.Date("2025-12-31"),
countries = "Spain",
date_breaks = "1 month"
)