MHASpread Documentation

MHASpread is a stochastic multiscale transmission model for simulating foot-and-mouth disease (FMD) and other multi-host pathogens across livestock farming networks.

Documentation Map

Technical Documentation

Model Overview — Model structure, compartments, and mathematical foundations
Transmission Dynamics — Within-farm dynamics, spatial kernel, species parameters
Control Strategies — Depopulation, vaccination, movement restrictions, contact tracing
Economic Impact Framework — Integration of epidemiological and economic modeling
Data Requirements — Input specifications and file formats

Learning Vignettes

Introduction — Getting started with MHASpread concepts
Model Structure — Detailed compartmental walkthrough
Transmission Processes — How infection spreads within and between farms
Control Strategies — Applying interventions effectively
Simulation Outputs — Interpreting model results
Case Studies — Real-world applications and lessons learned

Community & Training

Events and Training — International workshops, capacity building, and resources

Quick Start

Start with the Introduction vignette to understand core concepts.
Read Model Overview and Transmission Dynamics for the technical details.
Use Data Requirements and Model Structure to prepare inputs.
Review Control Strategies and Case Studies for applied examples.

Key Concepts

Concept	Description
Compartmental model	SEIR framework adapted for multiple host species with vaccination and depopulation compartments
Multiscale integration	Coupled within-farm and between-farm transmission processes
Stochastic simulation	Explicit uncertainty in transmission, detection, and control efficacy
Spatial kernel	Exponential distance-decay function for local disease spread (max 40 km)
Species specificity	Differential beta patterns reflecting biological differences (swine > cattle > small ruminants)
Evidence-based parameters	Transmission and disease duration parameters derived from peer-reviewed literature

MHASpread explicitly models:

Cattle (Bovine): Moderate transmitters; ~3-4 day infectious period
Swine: High transmitters (~5-15x more efficient than cattle); ~5-6 day infectious period
Small ruminants: Low transmitters; ~3 day infectious period

Farms can contain any combination of these species with homogeneous within-farm mixing.

Control Architecture

The model implements a three-zone containment strategy:

Scenario Outbreak
    ↓
[INFECTED ZONE] (3 km) → Depopulation + Vaccination + Surveillance
         ↓
    [BUFFER ZONE] (7 km) → Vaccination + Surveillance
         ↓
    [SURVEILLANCE ZONE] (15 km) → Detection + Contact Tracing

Frequently Asked Questions

Who should use MHASpread?

Veterinary epidemiologists conducting outbreak response research
Policy makers evaluating control strategy effectiveness
International organizations supporting disease surveillance
Academic researchers studying multi-host disease dynamics
Capacity-building institutions training epidemiologists in infectious disease modeling

What software do I need?

MHASpread is implemented as an R package. You will need:

R (version >= 4.0)
R packages: Core dependencies documented in the package DESCRIPTION file
Basic computing resources: Most simulations run on standard laptops

Can I use MHASpread for diseases other than FMD?

MHASpread is parameterized for FMD but can be adapted to other multi-host pathogens. Key adaptations needed:

Species-specific transmission coefficients (beta)
Disease duration parameters (latent and infectious periods)
Control strategy applicability
Spatial transmission kernel shape

Contact the developers for guidance on adaptation.

How do I prepare my data?

Detailed data preparation instructions are in Data Requirements. In brief:

Population file: Farm-level host species counts and GPS coordinates
Movements file: Animal shipments between farms (date, sender, receiver, species, count)
Control scenario file: Depopulation and vaccination capacity, detection parameters

Citation

If you use materials from this documentation, please cite:

Cardenas, N. C., Lopes, F. P. N., Machado, A., Maran, V., Trois, C., Machado, F. A., & Machado, G. (2024). Modeling foot-and-mouth disease dissemination in Rio Grande do Sul, Brazil and evaluating the effectiveness of control measures. Frontiers in Veterinary Science, 11, 1468864. https://doi.org/10.3389/fvets.2024.1468864

License

This documentation is provided as educational material. Code and software implementations are subject to separate licensing terms. See the LICENSE file in the repository for details.

Contact and Support

For questions about MHASpread documentation and methodologies:

Machado Lab — NC State University
https://machado-lab.github.io/

For technical support with model implementation:

Nicolas Cespedes Cardenas — ORCID