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45 changes: 45 additions & 0 deletions experiments/phase1/reports/parameter_description.md
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# Parameter value sources and justification
Updated for phase 1 calibration as of April 28th, 2026

## Parameter Descriptions

| Parameter | Description |
|-------------------------------|-------------------------------------------------------------------------------------------------|
| `infectiousness_rate_fn` | Constant rate of infection attempts generated by each infectious individual over the duration of infectiousness |
| `symptomatic_reporting_prob` | the probability that an infectious individual that is currently symptomatic is reported upon being imported into the population |
| `probability_mild_given_infect` | Probability a person develops any symptoms given that they were infected. Equivalent to one minus the asymptomatic probability. |
| `probability_{symptom_B}_given_{symptom_A}` | Probability a person with symptom category A transitions to the next ordered symptom severity category B, stratified by age group. |
| `{symptom_A}_to_{symptom_B}_delay` | Log-normal delay distribution parameters for the transition from symptom cateogry A to symptom category B, given that the individual is selected to progress along the illness severity timeline. |
| `{symptom_A}_to_resolved_delay` | Log-normal delay distribution parameters for the transition from illness with symptom category A to resolution.|
| `settings_properties` | Properties of settings, including the density-dependence scaling factor (`alpha`). |
| `itinerary_ratios` | Default proportion of time individuals spend in specific setting categories. |
| `prevalence_report` | Configuration for the prevalence report, including whether to write, filename, and period. |
| `incidence_report` | Configuration for the incidence report, including whether to write, filename, and period. |
| `transmission_report` | Configuration for the transmission report, including whether to write and filename. |
| `aggregated_deaths_report` | Configuration for the aggregated deaths report, including whether to write, filename, and period.|
| `first_death_terminates_run` | Boolean indicating whether the simulation terminates upon the first observed death. |

## Parameter Values

| Parameter | Value or Prior | Value Source |
|-------------------------------|------------------------------------------------------------------------------------------------|--------------|
| `infectiousness_rate_fn (rate)` | `LogNormal (mean -1.5, std_dev 0.5)` | Scaled to duration in order to produce an $R_0$ of approximately 2.1 |
| `infectiousness_rate_fn (duration)` | `12.0` | Generation interval maximum |
| `symptomatic_reporting_prob` | `Beta (alpha 5, beta 5)` | Perkins et al. 2020 |
| `probability_mild_given_infect` | `Beta (alpha 7, beta 3)` | Reasonable prior belief that 60%-80% of individuals will develop symptoms |
| `probability_dead_given_critical (Age0To17)` | `0.026` | CDC COVID-19 scenarios documents |
| `probability_dead_given_critical (Age18To49)` | `0.111` | CDC COVID-19 scenarios documents |
| `probability_dead_given_critical (Age50To64)` | `0.292` | CDC COVID-19 scenarios documents |
| `probability_dead_given_critical (Age65Plus)` | `0.699` | CDC COVID-19 scenarios documents |
| `critical_to_dead_delay (mu)` | `2.565` | CDC COVID-19 scenarios documents |
| `critical_to_dead_delay (sigma)` | `0.814` | CDC COVID-19 scenarios documents |
| `critical_to_resolved_delay (mu)` | `2.565` | CDC COVID-19 scenarios documents |
| `critical_to_resolved_delay (sigma)` | `0.814` | CDC COVID-19 scenarios documents |
| `settings_properties (Home)` | `Uniform(0, 1)` | No prior belief on at-home density-dependent transmission |
| `settings_properties (Work)` | `{"alpha": 0.0}` | No density-dependent transmission outside the home |
| `settings_properties (School)` | `{"alpha": 0.0}` | No density-dependent transmission outside the home |
| `settings_properties (Community)` | `{"alpha": 0.0}` | No density-dependent transmission outside the home |
| `itinerary_ratios (Home)` | `0.25` | Preliminary value to split time evenly across settings |
| `itinerary_ratios (Work)` | `0.25` | Preliminary value to split time evenly across settings |
| `itinerary_ratios (School)` | `0.25` | Preliminary value to split time evenly across settings |
| `itinerary_ratios (Community)` | `0.25` | Preliminary value to split time evenly across settings |
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