Within-Herd Transmission

Simulation of an FMDV spread between cattle in a herd

Description

The challengeABM package includes the simulate_within_herd() function that is calibrated to exhibit the same within-host virus dynamics as the simulate_room_to_room() function uses for laboratory based animal experiments. At simulation start, cattle (agents) are populated to a common area with a specified number of FMDV infected individuals. On simulation hour 1, cattle begin making random contact with each other at a specified hourly rate to show homogeneous mixing.

Depending on the quantity of virus in the donor cattle and chance contacts, they may or may not infect others. The quantity of virus in nasal passages and in blood serum has been calibrated to match the experimental study described in the analysis with parameters recorded in the default_herd_config.yaml configuration file that is available with this script.

challengeABM Package

Simulation code is available here: challengeABM. The GitHub site includes an Overview, Design concepts, Details document.

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# library(remotes)
# remotes::install_github("geoepi/challengeABM")

library(challengeABM)

Run the simulation

Set random seed for reproducible runs.

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seed_val <- round(runif(1, 100, 1000),0)
seed_val 

[1] 223

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set.seed(seed_val)

Run the simulation based using a configuration file with required parameters. Saving a copy for fast reloading of demo results.

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model_result <- simulate_within_herd(here("config/base_config_fmdv.yaml"),
                                     num_donors = 2,
                                     preclin_infect = TRUE,
                                     contact_rate = 0.25,
                                     seed = seed_val)

saveRDS(model_result, here("local/demo/model_result_herd_2025-06-13.rds"))

Download saved copy from OSF

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osf_id <- osf_project_demo %>%
  osf_ls_files() %>%
  filter(name == "model_result_herd_2025-06-13.rds") # file to download

osf_download(osf_id,
             path = here("local/temp"), # where to save
             conflicts = "overwrite")

name	id	local_path	meta
model_result_herd_2025-06-13.rds	684cc2c7559e9edbf0cc2c08	local/temp/model_result_herd_2025-06-13.rds	model_result_herd_2025-06-13.rds , file , /684cc2c7559e9edbf0cc2c08 , 465971 , osfstorage , /model_result_herd_2025-06-13.rds , 1749861063 , 1749861063 , c8e7d13d7d139db24cd1ae834761c9e9 , fd1ffdfec2a6406130aada6808b7f46343654eb8f2951d0b8c78147ffd5b190b , 0 , TRUE , 1 , FALSE , https://api.osf.io/v2/files/684cc2c7559e9edbf0cc2c08/ , https://files.osf.io/v1/resources/qf2wr/providers/osfstorage/684cc2c7559e9edbf0cc2c08 , https://files.osf.io/v1/resources/qf2wr/providers/osfstorage/684cc2c7559e9edbf0cc2c08 , https://files.osf.io/v1/resources/qf2wr/providers/osfstorage/684cc2c7559e9edbf0cc2c08 , https://osf.io/download/684cc2c7559e9edbf0cc2c08/ , https://mfr.osf.io/render?url=https%3A%2F%2Fosf.io%2Fdownload%2F684cc2c7559e9edbf0cc2c08%2F%3Fdirect%26mode%3Drender, https://osf.io/qf2wr/files/osfstorage/684cc2c7559e9edbf0cc2c08 , https://api.osf.io/v2/files/684cc2c7559e9edbf0cc2c08/ , https://api.osf.io/v2/files/684cb2aed0a256104638874a/ , 684cb2aed0a256104638874a , files , https://api.osf.io/v2/files/684cc2c7559e9edbf0cc2c08/versions/ , https://api.osf.io/v2/nodes/qf2wr/ , qf2wr , nodes , https://api.osf.io/v2/nodes/qf2wr/ , nodes , nodes , qf2wr , https://api.osf.io/v2/files/684cc2c7559e9edbf0cc2c08/cedar_metadata_records/

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# read save file to environment
model_result <- readRDS(here("local/temp/model_result_herd_2025-06-13.rds"))

Within-Host Dynamics

Randomly select 21 of 100 simulated animals to view nasal and virus quantities.

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plot_individual_virus_loads(model_result, sample_n = 21)

Herd Outbreak Curve

Compare the number of infected and recovered individuals.

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plot_herd_curve(model_result)