add documentation on symptom status manager

Author: eqmooring

docs/parameters.md

@@ -19,6 +19,27 @@ Other parameters, such as report generation and maximum runtime do not affect mo
 - `settings_properties.Any.alpha`: The density-dependence scaling factor of the total infection attempt rate for a particular setting. See [transmission](transmission.md) for more details.
 - `itinerary_ratios`: The default proportion of time individuals will spend in a specific setting category.
 
+## Symptom status parameters
+The following input parameters characterize the progression of illness in infected individuals. The parameters specify the probability of progressing to a particular state (mild, severe, critical, and dead) and specify the delay distributions (assumed to be log normally distributed) for each progression.
+- `probability_mild_given_infect`: Probability an infected person develops mild illness
+- `infect_to_mild_mu`: Mu parameter for log normal delay distribution from infection to mild illness
+- `infect_to_mild_sigma`: Sigma parameter for log normal delay distribution from infection to mild illness
+- `probability_severe_given_mild`: Probability a person with mild illness develops severe illness
+- `mild_to_severe_mu`: Mu parameter for log normal delay distribution from mild to severe illness
+- `mild_to_severe_sigma`: Sigma parameter for log normal delay distribution from mild to severe illness
+- `mild_to_resolved_mu`: Mu parameter for log normal delay distribution from mild illness to resolution
+- `mild_to_resolved_sigma`: Sigma parameter for log normal delay distribution from mild illness to resolution
+- `probability_critical_given_severe`: Probability a person with severe illness develops critical illness
+- `severe_to_critical_mu`: Mu parameter for log normal delay distribution from severe to critical illness
+- `severe_to_critical_sigma`: Sigma parameter for log normal delay distribution from severe to critical illness
+- `severe_to_resolved_mu`: Mu parameter for log normal delay distribution from severe illness to resolution
+- `severe_to_resolved_sigma`: Sigma parameter for log normal delay distribution from severe illness to resolution
+- `probability_dead_given_critical`: Probability a person with critical illness dies
+- `critical_to_dead_mu`: Mu parameter for log normal delay distribution from critical illness to death
+- `critical_to_dead_sigma`: Sigma parameter for log normal delay distribution from critical illness to death
+- `critical_to_resolved_mu`: Mu parameter for log normal delay distribution from critical illness to resolution
+- `critical_to_resolved_sigma`: Sigma parameter for log normal delay distribution from critical illness to resolution
+
 ## Model execution parameters
 The following parameters specified in the input parameter dictionary are relevant to model output and execution, but do not affect dynamics. All report variables can be turned off using `"write": false` in the input file.
 

docs/symptom_status.md

@@ -0,0 +1,6 @@
+# Symptom Status
+The symptom status module controls the progression of illness in infected individuals. `SymptomStatus` takes 1 of 6 values: `NoSymptoms` (the default), `Mild`, `Severe`, `Critical`, `Resolved`, or `Dead`. The progression to worse symptoms is a nested hierarchy: Individuals must pass through the mild state to reach severe, mild and severe states to reach critical, and so on. Consequently, probabilities are defined conditional on being in the previous state (e.g., probability of developing critical illness *given that the infected person has already developed severe illness*). However, the process of symptom resolution is not nested; individuals transition directly from the mild, severe, or critical states to the resolved state. Mild, severe, and critical are necessarily transitory states. All infected persons either remain in the `NoSymptoms` state (i.e., their infection was asymptomatic) or end up in the resolved or dead states. In addition to the conditional probabilities of progression, each transition is parameterized with a negative binomial delay distribution (parameters $\mu$ and $\sigma$).
+
+In the context of this module, we use the term "symptoms" generally to refer to the acute effects of SARS-CoV-2 infection on a person's health status, inclusive of both clinical signs and symptoms. Broadly speaking, mild illness corresponds to illness that can be managed at home and with outpatient care, hospitalization is a proxy for severe illness, and ICU admission is a proxy for critical illness. However, symptom statuses and presence in a particular clinical setting (hospital or ICU) are conceptually distinct. For example, in the context of high demand for care, there may be some critical patients for whom ICU care is indicated but are unable to access it. This module focus exclusively on modeling symptom status; it does not explicitly model healthcare seeking or the effects of interventions.
+
+In the current implementation, there is no correlation between symptom status progression and infectiousness (e.g., shorter time from infection to symptom onset is not correlated with shorter time from infection to infectiousness).