A dataframe containing results used to compare degrees of introduction,
spread, prevalence, persistence and cumulative infections of SARS-CoV-2 in
simulated white-tailed deer populations with an initial infection of 1 in
1000 deer on day 0. These results do not include continuous human
introduction during the 120-day fall simulation, and thus represent the risk
of single introductions to spawn persisting infections in white-tailed deer.
1000 iterations (run_id) were run for each scenario (Context). Scenarios
included captive deer in outdoor ranch facilities, captive deer in intensive
facilities, wild deer in rural areas, and wild deer in suburban areas.
Setting indicates whether deer were captive or wild. r0, or basic
reproductive number, indicates the number of secondary infections caused by a
single infectious deer over the course of it's infection. Prevalence is the
percent of a population infected, averaged over a simulated 120-day
projection. Persistence is a logical condition indicating if equilibrium
determined by SIRS ODE equations and run_steady() from the rootSolve
package predicts at least 1 in 1,000 deer infected at equilibrium. Cumulative
infections reports the total proportion of the population infected over the
course of the 120-fall projection, and can exceed 1, indicating that all
individuals were infected at least once during the fall season.
Format
initial_infection_results_1_in_1000
A data frame with 7 columns and 4000 rows storing the results of outbreak
simulations given an initial infection of 0.1% of deer. Each row corresponds
to an iteration of the simulation, with a specific Context and random draw of
epidemiological parameters:
- run_id
Identifier of run iteration
- Context
Scenario of focus for iteration
- Setting
Iteration is taking place with wild or captive deer
- r0
Basic reproductive number of iteration
- Prevalence
Average daily proportion of deer population that is infected
- Persist
Logical value for an outbreak persisting in a population at equilibrium
- Cumulative_infections
Total proportion of deer infected over the course of the 120-day fall simulation
Source
Derived from SIRS_analysis_by_contexts_initialspill.Rmd, to be
compared with continual introduction results from
SIRS_analysis_by_contexts.Rmd
Examples
if (FALSE) {
head(initial_infection_results_1_in_1000)
}