In bcgov/epi.branch.sim: Simulates an Epidemic Outbreak with a Branching Process

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This vignette provides detailed descriptions of the columns in the two output data frames, state_df and record_df. It is recommended to first read the introductory vignette as well as the first example vignette before diving into this one. For a detailed description of all input parameters, see the parameters vignette.

Contents of `state_df` data frame

This data frame is a "state vector" that evolves over time and only contains cases that are still actively influencing the simulation. When cases are isolated or inactive, they are removed from this data frame.

Entries with a * to the left of the column name are also present in the record_df data frame with the same name and entries marked by ** are present with a slightly modified name or meaning.

Contents of `record_df` data frame

This data frame is a complete record for all cases that ever existed in the simulation. As cases evolve over time, this data frame is updated and information is appended. Information is never removed or overwritten, with the exception of the s_status column, which is updated to the case's current state.

Entries with a * to the left of the column name are also present in the state_df data frame with the same name and entries marked by ** are present with a slightly modified name or meaning.

| | Column name | Data type | Description | | :-: | :---------- | :-------- | :---------- | | * | case_id | Integer | Unique identification number for each case | | | source | String | Either a string equal to the index case's case_id or "imported" if this case was imported. | * | is_traced | Boolean | Flag for whether case is manually traced | | * | is_trace_app_user | Boolean | Flag for whether case uses a contact tracing app | | * | is_traced_by_app | Boolean | Flag for whether case is traced by app (requires both index case and this case having is_trace_app_user=TRUE) |
| * | is_trace_app_comply | Boolean | Flag for whether case would comply with contact tracing app isolation instructions | | * | is_symptomatic | Boolean | Flag for whether case is symptomatic | | | d_incub | Double | Case incubation period, in days. Same as incubation_length in state_df. | | | d_iso_delay | Double | Case isolation delay time, measured in days from symptom onset time. Same as isolation_delay in state_df. | | | d_infection | Double | Case total infection duration, measured in days from start of infection. Same as infection_length in state_df. | | * | contact_rate | Double | Case relative contact rate, where 1 is the normal contact rate. Should be a value between 0 and 1, inclusive. | | | n_sec_infects | Integer | Number of total secondary infections with this case as the index case. In state_df, the column with the same name is a counter of outstanding secondary infections and decreases by one for every new secondary infection generated by this case. | | | d_generation_ints | Double, or vector of doubles | A list of all generation intervals corresponding to the all secondary infections where this case is the index case. In state_df, the column generation_intervals serves a similar purpose but only contains information for secondary infections yet to happen. Takes value numeric(0) when there are no outstanding secondary infections. | | | t_inf | Double | Simulation time-step where case was added. Meant for debugging and rather than analysis. | | | t_symp | Double | Simulation time-step where case status changed to symptomatic. Takes value NA if this status is never reached. Meant for debugging and rather than analysis. | | | t_iso | Double | Simulation time-step where case status changed to isolated. Takes value NA if this status is never reached. Meant for debugging and rather than analysis. | | | t_inact | Double | Simulation time-step where case status changed to inactive. Takes value NA if this status is never reached. Meant for debugging and rather than analysis. | | | cases_inf| NA | Placeholder for a vector of doubles containing the case_id for all secondary infections with this case as the index case. Not yet implemented, so the value is currently always NA. | | | s_status | String | One of incubation, symptomatic, asymptomatic, isolated or inactive for the case's current status. More details in the introductory vignette. Same as status in state_df. | | * | non_infect_generations | Double, or vector of doubles | A list of generation intervals for potential secondary infections that were prevented due to interventions such as case isolation and/or potential infections with generation intervals beyond the infection_length. Takes value numeric(0) when there are no prevented secondary infections. |