PARAMETRA

Welcome to the PARAMETRA livestock disease transmission database. This database has been assembled by the BIOSECURE consortium to facilitate livestock disease transmission modelling.

Overview

The PARAMETRA database is designed to be directly downloaded into programming environments such as R. It currently contains parameter values for up to 20 different livestock diseases, populated using a semi-systematic literature review.

For further information on methodology, please consult the accompanying publication [doi: XXXX - add when we submit to Biorxiv].

Database Structure

The PARAMETRA database is subdivided by disease and by parameter. Parameters included in the database are:

1. Transmission: Reproduction number, transmission parameter, probability of infection given direct/indirect contact, probability of reactivation of latent infection, other
2. Infectious/Latent/Incubation: Infectious period, latent period, incubation period, shape, other
3. Pathogen survival: Summary of relevant publications relating to pathogen survival on various surfaces and disinfection procedures
4. Diagnostic Test: Specificity, sensitivity
5. Within Herd Prevalence: Within herd prevalence
6. Regional Prevalence: Herd prevalence, global prevalence
7. Control Plan: Summary of relevant publications relating to voluntary or compulsory national and regional control plans
8. Other Relevant Information: Summary of publications relevant for modelling
9. LOT (List of Terms): List of terms used in the database and their meanings
10. Endemic pathogens: List of endemic pathogens and parameter availability summary
11. Epidemic pathogens: List of epidemic pathogens and parameter availability summary
12. AMR pathogens: List of antimicrobial resistance pathogens and parameter availability summary

Folders and Files

data/ : Contains all parameter value data in separate .csv files and the full database as a single .xlsx file.

outputs/: Contains the matrix summarizing the database contents, in excel and csv format.

Usage

The database and individual sheets can be downloaded directly into R or other programming environments. The database is designed to be used in the development of transmission models for livestock diseases.

How to download parametra csv files in R

1. Go to the CSV file

2. Click on the raw option present on the top right of the data

3. Copy de link (it starts with https://raw.githubusercontent.com/...)

To download just one table you can use the following code:

data<-read.csv("https://raw.githubusercontent.com/..")

To download and name multiple tables you can use the following code:

table_names<-c("Transmission", "InfectiousLatentIncubatperiod", "PathogenSurvival","DiagnosticTest","WithinHerdPrevalence", "RegionalPrevalence", "ControlPlan", "OtherRelevantInformation", "LOT", "ChangesLog", "Endemic_Pathogens", "Epidemic_Pathogens", "AMR_Pathogens")               

for(i in 1:lenght(table_names)){
  table_i<-read.csv(paste0("https://github.com/BIOSECURE-EU/parametra/blob/main/data/",table_names[i]))
  assign(table_names[i],table_i)
}

Database Modification

The database can only be modified by administrators. If you wish to make a modification, notice an error, or would like to include an additional disease or parameter, please contact the administrators.

Contact

• Natalia Ciria Artiga: [email protected]
• Alistair Antonopoulos: [email protected]

License

Acknowledgments

This open source software code was developed the BIOSECURE Project, funded from the European Union’s HORIZON Europe FARM2FORK project.