Pathogens

Pathogen <: Parameter

A type representing a pathogen.

Instantiation

The instantiation requires at least an id and a name that must be supplied as keyword arguments. All other fields are optional parameters.

covid = Pathogen(id = 1, name = "COVID19")
flu = Pathogen(id = 2, name = "Flu", onset_of_symptoms = Poission(3))

Parameters

• id::Int8: Unique identifier pathogen
• name::String: Name of the pathogen
• dpr::DiseaseProgressionStrat = DiseaseProgressionStrat() (optional): Defines the distribution of symptom categories across age groups
• infection_rate::Distribution = Uniform(0,1) (optional): Distribution of the infection rate
• mild_death_rate::Distribution = Uniform(0,0.005) (optional): Distribution of the death rate for mild cases
• severe_death_rate::Distribution = Uniform(0,0.1) (optional): Distribution of the death rate for severe cases
• critical_death_rate::Distribution = Uniform(0,0.1) (optional): Distribution of the death rate for critical cases
• hospitalization_rate::Distribution = Uniform(0, 0.1) (optional): Distribution of the probability for a severe case to be hospitalized
• ventilation_rate::Distribution = Uniform(0, 0.1) (optional): Distribution of the probability for a critical case to need ventilation
• icu_rate::Distribution = Uniform(0, 0.1) (optional): Distribution of the probability for a critical case to need ICU
• onset_of_symptoms::Distribution = Uniform(2,3) (optional): Distribution of time till onset of symptoms from becoming exposed
• onset_of_severeness::Distribution = Uniform(2,3) (optional): Distribution of time till onset of severeness from onset of symptoms
• infectious_offset::Distribution = Uniform(0,1) (optional): Distribution of the offset to become infectious compared to the onset of symptoms
• time_to_hospitalization::Distribution = Uniform(0,1) (optional): Distribution of time till hospitalization from onset of symptoms
• time_to_icu::Distribution = Uniform(0,1) (optional): Distribution of time till ICU from hospitalization
• time_to_recovery::Distribution = Uniform(5,6) (optional): Distribution of time till recovery from becoming exposed
• length_of_stay::Distribution = Uniform(6,7) (optional): Distribution of time duration to stay in hospital

DiseaseProgressionStrat <: AgeStratification

A wrapper type for an age stratification matrix regarding the disease progression.

Fields

• age_groups::Vector{String}: A list of the age groups in order of the rows of the stratification matrix. The first entry in age_groups belongs to the first row in the matrix.
• disease_compartments::Vector{String}: A list of the compartments/terminal states in the disease progression in order of the columns of the stratification matrix. First entry in disease_compartments belongs to the first column in the stratification matrix.
• stratification_matrix::Vector{Vector{T}} where T <: Real: The matrix that holds the probabilities for the age stratified disease progression. The entries of each row have to add up to 1.

critical_death_rate(pathogen::Pathogen)

Returns the death rate (distribution) of the pathogen in the case of critical progression.

DiseaseProgressionStrat()

A constructor for a default Disease Progression, where every individual will only be assigned to be asymptomatic. Mainly for testing purposes.

disease_progression_strat(pathogen::Pathogen)

Returns the stratified probabilities for disease progression.

hospitalization_rate(pathogen::Pathogen)

Returns the hospitalization rate (distribution) of the pathogen in the case of a severe disease progression.

icu_rate(pathogen::Pathogen)

Returns the icu rate (distribution) of the pathogen in the case of a critical disease progression.

id(pathogen::Pathogen)

Returns the id of the pathogen.

infection_rate(pathogen::Pathogen)

Returns the infection rate (distribution) of the pathogen.

infectious_offset(pathogen::Pathogen)

Returns the time distribution for the offset of becoming infectious, before developing symptoms.

length_of_stay(pathogen::Pathogen)

Returns the time distribution of the duration an individual will be hospitalized.

mild_death_rate(pathogen::Pathogen)

Returns the death rate (distribution) of the pathogen in the case of mild symptoms.

name(pathogen::Pathogen)

Returns the name of the pathogen.

onset_of_severeness(pathogen::Pathogen)

Returns the time distribution for the onset of severe symptoms.

onset_of_symptoms(pathogen::Pathogen)

Returns the time distribution for the onset of symptoms.

sample_critical_death_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the death rate distribution for critical disease progressions.

sample_hospitalization_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the hospitalization rate distribution.

sample_icu_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the ICU rate distribution.

sample_infectious_offset(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the infectious offset distribution.

sample_length_of_stay(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the time_to_hopsitalization distribution for cases with severe disease progression.

sample_mild_death_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the death rate distribution for cases with mild symptoms.

sample_onset_of_severeness(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the onset_of_symptoms distribution.

sample_onset_of_symptoms(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the onset_of_symptoms distribution.

sample_self_quarantine_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the ICU rate distribution.

sample_severe_death_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the death rate distribution for severe disease progressions.

sample_time_to_hospitalization(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the time_to_hospitalization distribution for cases with severe disease progression.

sample_time_to_icu(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the time_to_icu distribution for cases with critical disease progression.

sample_time_to_recovery(pathogen::Pathogen,  indiv::Individual)

Returns a randomly drawn (rounded) value from the time_to_recovery distribution.

sample_ventilation_rate(pathogen::Pathogen, indiv::Individual)

Returns a randomly drawn value from the Ventilation rate distribution.

severe_death_rate(pathogen::Pathogen)

Returns the death rate (distribution) of the pathogen in the case of severe symptoms.

time_to_hospitalization(pathogen::Pathogen)

Returns the distribution for the time till hospitalization starting from the onset of symptoms.

time_to_icu(pathogen::Pathogen)

Returns the distribution for the time till ICU starting from the hospitalization time.

time_to_recovery(pathogen::Pathogen)

Returns the time to recovery (distribution) of the pathogen.

transmission_function!(pathogen::Pathogen, transFunc::TransmissionFunction)

Returns the transmission_function for the pathogen.

transmission_function(pathogen::Pathogen)

Returns the transmission_function for the pathogen.

ventilation_rate(pathogen::Pathogen)

Returns the ventilation rate (distribution) of the pathogen in the case of a critical disease progression.