Replication Data for: Revealing mechanisms of infectious disease transmission through empirical contact networks

Edgelist and infection time series files for the two empirical datasets used in the study. The first dataset comprises of dynamic networks of bee colonies (5-7 individuals), where edges represent direct physical contacts that were recorded using a color-based video tracking software. Progression of infection by Crithidia bombi through the colonies was tracked by daily screening of individual feces, and the infection timing was determined using the knowledge of the rate of replication of C. bombi within its host intestine. In addition to citing this dataset and the article, please also cite the original publication that describes the data: Otterstatter, Michael C., and James D. Thomson. "Contact networks and transmission of an intestinal pathogen in bumble bee (Bombus impatiens) colonies." Oecologia 154.2 (2007): 411-421. The second dataset monitors the spread of the commensal bacterium Salmonella enterica in two separate wild populations of the Australian sleepy lizard Tiliqua rugosa. The two sites consisted of 43 and 44 individuals respectively, and these represented the vast majority of all resident individuals at the two sites (i.e., no other individuals were encountered during the study period). Individuals were fitted with GPS loggers and their locations were recorded every 10 minutes for 70 days. Salmonella infections were monitored using cloacal swabs on each animal once every 14 days. Consequently, the disease data in this system do not identify the onset of each individual's infection. Column headers of the edgelist file : Note that the edges in edgelist are undirected (i.e., there is no direction associated with the edges) node1: Id of the first individual involved in the interaction node2: Id of the second individual involved in the interaction timestep: The time step of the interation (measured in days) weight_freq: The frequency of interactions between the individuals at that time step weight_dur: The duration of interactions between the individuals at that time step (measured in seconds) Column headers of the infection data files : Node: Id of the individual timestep: Time step of the infection diagnosis (measured in days) diagnosis: infection diagnosis. 0 indicates that the individual was diagnosed to be uninfected and 1 indicates that the individual was diagnosed to be infected. Note that for some datasets, infection diagnoses at all time steps were not available.