SNA

Social Network Analyses - Analysis of social contacts in confined indoor environments.

The aim of this repository is to collect the analyses performed by the CSI:DT research group to better understand social interactions and animal movement in dairy cows. The focus of this repository will be on R, using a variety of functions and packages to study animal movement, social behavior and time budgets in dairy cows.

Content

Core methods to analyse social contact data:

• scripts/stERGM_tutorial.Rmd: This stERGM tutorial replicates the analysis performed in Marina et al. (2023), Rmarkdown version.

• scripts/stERGM_tutorial.html: This stERGM tutorial replicates the analysis performed in Marina et al. (2023), html version.

Animal raw and processed files:

• data/raw/Phenotypes_LateLactationGroup.csv: Information about the dairy cows.

• data/raw/Interactiondata/ : This folder contains the adjacency matrices, computed independently for each functional area ("FeedingArea","RestingArea") and each day (i.e., 24 h) of the 14 days considered in this study using position data.

• data/raw/Relationshipdata/: This folder contains the kindergarten effect matrix, the lactational effect matrix and the additive relationship matrix calculated from the pedigree.

• data/processed/Figure1.jpg: Schematic map of the free-stall barn.

Output obtained from the analyses:

• output/Figure2_FA.gif: Animated transition between the social networks detected in the feeding area.

• output/Figure2_RA.gif: Animated transition between the social networks detected in the resting area.

Participants in the CSI:DT project

• 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)

Contributing

Pull requests are welcome. Please make sure to update tests as appropriate.

License

SLU