ervissexplore

An R package to easily retrieve ERVISS (European Respiratory Virus Surveillance Summary) data from the EU-ECDC. Provides functions to fetch, filter, and optionally visualize respiratory virus surveillance data across European countries.

Please visit https://erviss.org/ for a detailed description of the underlying data (see ‘Methods’ in the footer).

Installation

install.packages("pak")
pak::pak("Epiconcept-Paris/ervissexplore")

Quick Start

library(ervissexplore)

# Retrieve SARS-CoV-2 positivity data
positivity_data <- get_sentineltests_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  pathogen = "SARS-CoV-2",
  countries = c("France", "Germany", "Italy")
)

head(positivity_data)
#>                 survtype countryname yearweek   pathogen pathogentype
#>                   <char>      <char>   <char>     <char>       <char>
#> 1: primary care sentinel      France 2024-W52 SARS-CoV-2   SARS-CoV-2
#> 2: primary care sentinel      France 2024-W52 SARS-CoV-2   SARS-CoV-2
#> 3: primary care sentinel      France 2024-W52 SARS-CoV-2   SARS-CoV-2
#> 4: primary care sentinel      France 2024-W51 SARS-CoV-2   SARS-CoV-2
#> 5: primary care sentinel      France 2024-W51 SARS-CoV-2   SARS-CoV-2
#> 6: primary care sentinel      France 2024-W51 SARS-CoV-2   SARS-CoV-2
#>    pathogensubtype  indicator    age value       date
#>             <char>     <char> <char> <num>     <Date>
#> 1:      SARS-CoV-2 detections  total   3.0 2024-12-23
#> 2:      SARS-CoV-2 positivity  total   2.1 2024-12-23
#> 3:      SARS-CoV-2      tests  total 142.0 2024-12-23
#> 4:      SARS-CoV-2 detections  total  13.0 2024-12-16
#> 5:      SARS-CoV-2 positivity  total   4.1 2024-12-16
#> 6:      SARS-CoV-2      tests  total 319.0 2024-12-16

Data Sources

The package fetches data directly from the EU-ECDC Respiratory Viruses Weekly Data repository.

Seven data sources are available:

Data source	Function	Description
Sentinel positivity	`get_sentineltests_positivity()`	Test positivity rates by pathogen
SARS-CoV-2 variants	`get_erviss_variants()`	Variant proportions and detections
ILI/ARI rates	`get_ili_ari_rates()`	ILI/ARI consultation rates by age group
SARI rates	`get_sari_rates()`	SARI hospitalisation rates by age group
SARI virological	`get_sari_positivity()`	SARI tests, detections and positivity
Non-sentinel severity	`get_nonsentinel_severity()`	Deaths, hospital and ICU admissions
Non-sentinel tests	`get_nonsentinel_tests()`	Non-sentinel tests and detections

A generic function get_erviss_data(type = ...) can also be used to access any of the above sources.

Latest Data vs Snapshots

By default, functions fetch the latest available data. For reproducibility, you can use historical snapshots:

# Use a specific snapshot for reproducible analyses
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")
)

To see available snapshot dates, visit the EU-ECDC Respiratory Viruses Weekly Data repository.

Examples

Retrieve and analyze data

# Get positivity data (returns a data.table)
data <- get_sentineltests_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-06-30"),
  pathogen = c("SARS-CoV-2", "Influenza"),
  countries = c("France", "Spain", "Italy"),
  indicator = "positivity"
)

# Your own analysis with data.table syntax
data[,
  .(
    min_positivity = min(value, na.rm = TRUE),
    mean_positivity = mean(value, na.rm = TRUE),
    max_positivity = max(value, na.rm = TRUE)
  ),
  by = .(countryname, pathogen)
]
#>    countryname   pathogen min_positivity mean_positivity max_positivity
#>         <char>     <char>          <num>           <num>          <num>
#> 1:      France  Influenza            0.0       19.223077           58.7
#> 2:      France SARS-CoV-2            0.0        8.942308           66.7
#> 3:       Italy  Influenza            0.6       12.670588           40.5
#> 4:       Italy SARS-CoV-2            0.0        2.247059           10.4
#> 5:       Spain  Influenza            0.2        7.361538           43.7
#> 6:       Spain SARS-CoV-2            0.8       10.626923           45.6

Other data sources

# ILI consultation rates
ili_data <- get_ili_ari_rates(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  indicator = "ILIconsultationrate",
  age = c("0-4", "65+"),
  countries = "France"
)

# Hospital admissions
severity_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 = c("France", "Spain")
)

# SARI positivity
sari_data <- get_sari_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  pathogen = "Influenza",
  indicator = "positivity",
  countries = "EU/EEA"
)

Using the generic function

# All sources accessible via a single function
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"
)

Visualization (optional)

The package includes optional plotting functions for quick exploration. They return ggplot2 objects that can be customized freely:

data <- get_sentineltests_positivity(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-06-30"),
  pathogen = "SARS-CoV-2",
  countries = c("France", "Spain"),
  indicator = "positivity"
)
plot_erviss_positivity(data, date_breaks = "1 month")

Or use the quick one-liners:

quick_plot_ili_ari_rates(
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31"),
  indicator = "ILIconsultationrate",
  countries = c("France", "Spain"),
  date_breaks = "1 month"
)

Using a local CSV file

# If you have downloaded the data locally
data <- get_erviss_variants(
  csv_file = "path/to/local/variants.csv",
  date_min = as.Date("2024-01-01"),
  date_max = as.Date("2024-12-31")
)

Main Functions

Data retrieval

Function	Description
`get_sentineltests_positivity()`	Sentinel test positivity rates
`get_erviss_variants()`	SARS-CoV-2 variant data
`get_ili_ari_rates()`	ILI/ARI consultation rates
`get_sari_rates()`	SARI hospitalisation rates
`get_sari_positivity()`	SARI virological data
`get_nonsentinel_severity()`	Non-sentinel severity data
`get_nonsentinel_tests()`	Non-sentinel tests/detections
`get_erviss_data()`	Generic function (all types)

Visualization (optional)

Function	Description
`plot_erviss_positivity()`	Plot positivity data
`plot_erviss_variants()`	Plot variant data
`plot_ili_ari_rates()`	Plot ILI/ARI rates
`plot_sari_rates()`	Plot SARI rates
`plot_sari_positivity()`	Plot SARI virological data
`plot_nonsentinel_severity()`	Plot severity data
`plot_nonsentinel_tests()`	Plot non-sentinel tests
`plot_erviss_data()`	Generic plot function
`quick_plot_*()`	Fetch + plot in one call

URL builders

Function	Description
`get_erviss_url()`	Generic URL builder (all types)
`get_sentineltests_positivity_url()`	Positivity data URL
`get_erviss_variants_url()`	Variants data URL
`get_ili_ari_rates_url()`	ILI/ARI rates URL
`get_sari_rates_url()`	SARI rates URL
`get_sari_positivity_url()`	SARI virological data URL
`get_nonsentinel_severity_url()`	Non-sentinel severity URL
`get_nonsentinel_tests_url()`	Non-sentinel tests URL

Contributing to `{ervissexplore}`

New contributors are welcome !

You can contribute to the package in many ways:

By reporting bugs, issues or feature requests: please open an issue on the GitHub repository.
By fixing bugs or improving the package: please clone or fork the repository, work on a dedicated branch and create a pull request.

Citation

European Centre for Disease Prevention and Control. European Respiratory Virus Surveillance Summary (ERVISS), 2026, Week 05. Available at https://erviss.org/.

ervissexplore

Installation

Quick Start

Data Sources

Latest Data vs Snapshots

Examples

Retrieve and analyze data

Other data sources

Using the generic function

Visualization (optional)

Using a local CSV file

Main Functions

Data retrieval

Visualization (optional)

URL builders

Contributing to {ervissexplore}

Citation

Contributing to `{ervissexplore}`