Skip to content

Latest commit

 

History

History
138 lines (98 loc) · 3.53 KB

room_to_room_transmission.md

File metadata and controls

138 lines (98 loc) · 3.53 KB

challengeABM: Room-to-Room Transmission

Description

The challangeABM package includes the simulate_room_to_room() function for simulating virus transmission between 18 head of cattle. At simulation start, cattle (agents) are divided among five isolated rooms, with two donor cattle in Room 1, and four cattle in each of the other rooms, Rooms 2-5. On simulation hour 1, the two donor cattle are inoculated by a virus. The donor cattle remain isolated from other cattle for a 24hr period, then at the 24hr mark, the donor cattle (now infected) are moved to Room 2. At the next 24hr interval (48 hours since start of simulation), the donor cattle leave Room 2 and proceed to Room 3, where they remain for a 24hr period. The process continues with donors moving to Room 4 at 72hrs and Room 5 at 96hrs.

Depending on the quantity of virus in the donor cattle, they may or may not infect others. The quantity of virus in nasal passages and in blood serum has been calibrated to replicate like Foot-and-Mouth Disease Virus (FMDV).

The status of individual cattle virus loads, clinical presentation, and other factors are recorded on an hourly basis.

Virus and cattle parameters may be specified in configuration files to simulate changes to infectivity and virulence. Eventually, simulate_room_to_room() will be updated to allow changes in time intervals (minutes, hours, days,…), the number of rooms, and the number of animals in each room.

Load challengeABM

Hide code 
library(challengeABM)

Run the simulation

First, set random seed for reproducible runs.

Hide code 
seed_val <- round(runif(1, 100, 300),0)
seed_val 
[1] 139
Hide code 
set.seed(seed_val)

Run the simulation based using a configuration file with needed parameters..

Hide code 
model_result <- simulate_room_to_room(here("config/default_R2R_config.yaml"))

Within-Host Dynamics

View change in nasal and virus quantities within individual animals.

Hide code 
plot_virus_loads_R2R(model_result)

Status of Individual Animals

View the disease status of individual animals.

Hide code 
plot_animal_status(model_result)

Iterate

Additional function for multiple iterations.

Hide code 
iterate_R2R(simulate_room_to_room, # function
            config_file = here("config/default_R2R_config.yaml"), # settings to run
            num_iterations = 50, # total iterations
            write_interval = 10, # write to csv every write_interval
            output_directory = here("local/test"), # where to write
            use_parallel = TRUE, num_cores = 8
)