A computational tool to simulate direct and environmental transmission of mastitis-causing bacteria in dairy cows. The computational tool simulates the transmission of pathogens using realistic social interaction and area utilisation information of dairy cows.
Core methods to simulate mastitis-causing bacteria transmission in dairy farms:
-
scripts/Direct_transmission.R: This tutorial simulates a direct transmission of mastitis-causing bacteria within a dairy farm following the prevalence of mastitis infection reported in Woudstra et al. (2023). Strain diversity and infection durations of Staphylococcus spp. and Streptococcus spp. causing intramammary infections in dairy cows and the social network structure reported in Marina et al. (2023). New insight into social relationships in dairy cows and how time of birth, parity, and relatedness affect spatial interactions later in life -
scripts/Enviromental_transmission.R: This tutorial simulates an environmental transmission of mastitis-causing bacteria within a dairy farm following the prevalence of mastitis infection reported in Woudstra et al. (2023) Reservoirs of Staphylococcus spp. and Streptococcus spp. Associated with Intramammary Infections of Dairy Cows and the area utilisation distribution reported in Marina et al. (2024). Multiple factors shape social contacts in dairy cows
The results show the average prevalence of susceptible (healthy), infected and, recovered animals over a simulated year. The shaded lines show the standard deviation of the simulated replicates:
- Lars Rönnegård (DU & SLU): Principal investigator.
- Per Peetz Nielsen (RISE)
- Carsten Kirkeby (KU)
- Volker Krömker (KU)
- Freddy Fikse (Växa Sverige)
- Anna Skarin (SLU)
- Moudud Alam (DU)
- Keni Ren (SLU)
- Maya Katrin Gussmann (KU)
- Svenja Woudstra (KU)
- Ida Hansson (SLU)
- Hector Marina (SLU)
Pull requests are welcome. Please make sure to update tests as appropriate.