This repo compiles into an epidemiological model, intended to model the spread and maintenance of Foot-and-Mouth disease (FMD) in the Republic of Turkey.
It requires data on villages/farms, and recorded cattle shipments to simulate this.
The data to be imported, and options to specify aspects of the disease and control policies implemented are specified in a YAML configuration file. By default, this configuration file is named config.yaml and will be looked for in the working directory of the executable. Other names and/or locations can be specified as a CLI options, e.g. ./model-binary ../inputs/different-config.yaml.
Three files act as inputs to the model.
- The config.yaml file
- A csv file describing the nodes (epi-units/villages) to be modelled,
node_filein config.yaml. - A csv file describing the shipments between nodes,
shipment_filein config.yaml
The node file should be in the format:
| ID | km north (double) | km east (double) | number of cattle (integer) |
Shipment records should be in the format:
| Day (integer) | source node ID | target node ID | number shipped (integer) |
Outputs are written to the directory specified by output_id.
By default, a csv file in the tidy format is output called $(output_id)-node-infection-report.csv. This file describes the incidence and prevalence for each combination of:
- run
- day
- serotype
- true/detected
Optionally other descriptive files can also be output, as described in the following table:
| Filename | Configuration option | Description |
|---|---|---|
| $(output_id)-infection-events.csv | infection_events |
A list of every transmission spread between nodes, including type of transmission event. |
| $(output_id)-global-compartment-sums.csv | compartment_sums |
A sum of the global population in each compartment, for every run, day and serotype. |
|
|
detailed_reports |
Reports the time since infected for each node, for each serotype and run. Output to $(output_directory)/detailed-reports |
Configuration of the model takes place in the configfile. The model will look for a file named config.yaml in the same directory as the executable.
Optionally, specifying a configuration file of another name and/or in another directory can be done via the CLI, such as:
./<model> <path-to-different-config> etc, so long as the normal options are present.
Make sure to preserve the structure of the file. E.g. node_file: should be under inputs:.
| Option | Type | Description |
|---|---|---|
inputs: |
- | ------------------------ |
node_file: |
String | Filename describing nodes to run on, as described in Inputs section. |
shipment_file: |
String | Filename describing shipments to run, as described in Inputs section. |
outputs: |
- | ------------------------- |
output_directory: |
String | Directory where all outputs will be written. |
output_id |
String | ID which all outputs will be prefixed with, to identify the relevant results. |
detailed_report: |
Boolean | Whether to output detailed reports. |
compartment_sums: |
Boolean | Whether to output global compartment sums. |
infection_events: |
Boolean | Whether to output infection events. |
verbosity: |
Integer | Console verbosity level 0-2, 0 is silent, 2 outputs everything. |
general: |
- | ------------------------- |
num_runs: |
Integer | The number of replicates of the model run. Should be > 0. |
start_day: |
Integer | The integer day to start each model run on. |
end_day: |
Integer | The integer day to end each model run on. Inclusive. |
model_options: |
- | ------------------------- |
run_shipments: |
Boolean | Whether user-provided animal shipments will happen. Note it will not read shipments_file if this is set to false. |
implement_burn_in: |
Boolean | Whether a burn-in run should happen. Burn-in is a discarded model run from which all normal runs will then proceed. |
burn_in_duration: |
Integer | If burn_in_implemented, how many days should the burn in period be? |
maternal_immunity: |
Boolean | Should maternal immunity be modelled? |
implement_force_infections: |
Boolean | Should there be a background force of infection which can possibly infect 1 uninfected node per day? |
forcing_rate: |
Double | The daily probability of a forced infection. |
max_node_infection_duration: |
Integer | How long can a Node realistically be infected for? Possibly will be deprecated, as this is only used when Nodes are remaining infected for completely unrealistic amounts of time. |
seeding: |
- | ------------------------- |
fixed_seed: |
Boolean | If true, reads from seed_nodes. If false, randomly seed number_random_seeds nodes |
number_random_seeds: |
Integer | The number of nodes to randomly seed if fixed_seed is false. Should be in interval [1, number of nodes] |
seed_nodes: |
List of Strings | A list of the Node IDs which should be seeded with infection at the beginning of each run (or burn-in). |
serotype: |
String | The serotype that each seed node will be seeded with. This needs to be present in disease->serotypes as well. |
population_parameters: |
- | ------------------------- |
birth_rate: |
Double | The daily rate at which births happen. |
mortality_rate: |
Double | The daily rate at which mortality unrelated to infection happens. |
disease: |
- | ------------------------- |
serotypes: |
List of Strings | The names of the serotypes to be modelled. |
$(serotype)_parameters: |
- | There should be one of these sections for each serotype specified in disease->serotypes. Each of the following parameters is specific to $(serotype). |
beta: |
Double | The within-node rate of infection. |
sigma: |
Double | The within-node rate of progression to infectious. Reciprocal of serotype's average latent period. |
gamma: |
Double | The within-node rate of recovery. Reciprocal of average infectious period. |
immunity_duration: |
Double | The average duration (in days) of natural immunity, i.e. from exposure to the actual disease. |
maternal_immunity_duration: |
Double | The average duration (in days) of maternal immunity. |
mortality: |
Double | The daily rate of infection related mortality. |
transmission: |
Double | The per-capita force of infection between-nodes. |
susceptibility: |
Double | The per-capita susceptiblity to transmission. Should be deprecated. |
shipments: |
- | Parameters for transmission via animal shipments. |
fomite_transmission_probability: |
Double | The percentage probability that disease is transmitted via fomites when a shipment originates from an infected Node. E.g. 1.0%, 5.0% etc... |
kernel: |
- | ------------------------- |
a: |
Integer | Kernel parameter. Do not change from 1. |
b: |
Double | Kernel parameter (shape or size?). |
c: |
Double | Kernel shape or size parameter. Needs to be 2.0 or greater. |
control_options: |
- | ------------------------- |
detection: |
- | ------------------------- |
detection_probability: |
Double | The per-infection probability of detecting an infection. Should be between 0 (cannot detect) and 100 (detect everything). |
detection_delay: |
Integer | The delay between a node becoming infected and the infection being detected, assuming it is detectable. |
vaccine: |
- | ------------------------- |
$(serotype): |
- | There should be a section describing the following parameters for each serotype in disease->serotypes. |
efficacy: |
Double | The average efficacy of the vaccine in producing protective immunity against this serotype. 0-100. |
efficacy_stdev: |
Double | The standard deviation to the efficacy. |
duration: |
Double | The average number of days that the protective immunity generated against $(serotype) lasts. |
daily_vaccination_capacity: |
Integer | The number of nodes which can be vaccinated in a day. |
reactive_vaccination: |
- | ------------------------- |
implement: |
Boolean | Should reactive vaccination be modelled? |
radius: |
Double | What radius around the detected infected node should be vaccinated? |
coverage: |
Double | What percentage of those in the radius are actually vaccinated? |
mass_vaccination: |
- | ------------------------- |
implement: |
Boolean | Should mass vaccination be modelled? |
interval: |
Integer | If mass vaccination is modelled, how many days are there between rounds of mass vaccination? |
coverage: |
Double | What percentage of nodes identified for mass vaccination are actually vaccinated? |
movement_ban_policy: |
- | ------------------------- |
implement: |
Boolean | Should a reactive movement ban around detected nodes be modelled? |
radius: |
Double | What radius around a detected node are banned from shipping cattle in or out? |
duration: |
Integer | How long does a movement ban last? |
compliance: |
Double | What percentage of nodes in the radius comply with the ban? |