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PARAMETRA

A curated database for animal disease modelling, that contains data on infectious periods, transmission rates, pathogen survival, diagnostic tests, prevalence, and control measures for multiple livestock diseases.

Originally developed by the BIOSECURE consortium through a semi-systematic literature review. For more information on the methodology, see the accompanying publication:

Antonopoulos, A., Ciria, N., Regan, Á., Tubay, J., Ciaravino, G., Hayes, B., Lambert, S., Vergne, T., Velkers, F., Biebaut, E., Viltrop, A., Dewulf, J., Charlier, J., Fischer, E., & Palau, A. A. (2025). PARAMETRA: A transmission modelling database for livestock diseases. Preventive Veterinary Medicine, 245, 106668. https://doi.org/10.1016/j.prevetmed.2025.106668

The database continues to grow thanks to user contributions via the PARAMETRA submission form.

The availability of parameters by pathogen, parameter type, year and study type can be visualized here.

How to use it

Download Excel file

Click here to download parametra as an Excel file. This file can also be found at data-raw/parametra.xlsx.

Installation as an R package 

# install.packages("devtools")
devtools::install_github("BIOSECURE-EU/parametra")

URL Data Access

Access the database and individual sheets directly in R or other programming environments for livestock disease transmission modeling.

Download CSV files in R

  1. Navigate to the CSV file in data-raw/tables
  2. Click raw in the top right
  3. Copy the link (starting with https://raw.githubusercontent.com/..)

Example: Download parametra_long.csv (containing all parameter tables) directly in R:

data<-read.csv("https://raw.githubusercontent.com/BIOSECURE-EU/parametra/refs/heads/main/data-raw/parametra_long.csv")

Or in Python:

import pandas as pd

data = pd.read_csv("https://raw.githubusercontent.com/BIOSECURE-EU/parametra/refs/heads/main/data-raw/parametra_long.csv")

Database Structure

Each PARAMETRA entry contains a parameter, pathogen, and reference. Additional information varies by parameter type and may include host species, study type, value, and upper and lower confidence intervals. It is organized in the following tables:

  1. transmission: Reproduction number, transmission parameter, probability of infection given direct/indirect contact, probability of reactivation of latent infection and other transmission parameters.
  2. infectious_latent_incuba_period: Infectious period, latent period, incubation period, shape and other disease period parameters.
  3. pathogen_survival: Survival parameters in different materials and environmental conditions
  4. diagnostic_test: Diagnostic test parameters such as test specificity and sensitivity.
  5. within_herd_prevalence: Within-herd pathogen prevalence parameters.
  6. regional_prevalence: Regional pathogen prevalence parameters at country or sub-division level.
  7. control_plan: Information about disease control programs and plans implemented in different countries.
  8. cost_biosecurity: Information about prices of products needed to implement biosecurity measures
  9. other: Additional parameters and information related to various infectious diseases in animal populations that do not fit into other specific categories

All this tables are aggregated in parametra_long. You can find their full documentation here.

Crossref

The parametra_crossref table contains bibliographic information found on Crossref for all references (“ref”) cited in the database.

Complementary tables

Only available in the excel file:

  1. LOT (List of Terms): List of terms used in the database and their meanings.
  2. CHANGELOG : Tracks modifications, updates, and version history.
  3. crossref: Metadata extracted from CrossRef using the rcrossref package for scientific publications referenced in the parametra_long dataset.

How to Submit New Parameters

There are two ways to contribute new parameters to the PARAMETRA database:

Option 1: Single Parameter Submission

  1. Visit the PARAMETRA submission form
  2. Fill in the required fields for your single parameter entry
  3. Submit the form

Option 2: Bulk Submission (Excel Template)

  1. Download the Excel template
  2. Fill out the Excel template with your parameter entries, using PARAMETRA database as a reference for proper formatting.
  3. Upload the file through the PARAMETRA submission form

All submissions will be reviewed by PARAMETRA administrators before being added to the database to ensure data quality and consistency.

Contact

contact@parametra.eu

Or directly to maintainers: natalia.ciria@uab.cat and alistair@kreavet.com

License

License: CC BY-SA 4.0

Acknowledgments

PARAMETRA was developed as part of the BIOSECURE Project, funded from the European Union’s HORIZON Europe FARM2FORK project.

Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or REA. Neither the European Union nor the granting authority can be held responsible for them.