Epidemic model



Tables: Parameter estimates

\(R(t)\), \(r(t)\), \(\alpha(t)\), \(\kappa(t)\), \(\delta(t)\), CFR(t), IFR(t)

CFR(t), IFR(t)

Prior and posterior parameter distributions

Plots for the prior distribution and estimated posterior distribution of each parameter at specific time intervals

\(R(t)\)

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\(r(t)\)

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\(\alpha(t)\)

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\(\kappa(t)\)

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\(\delta(t)\)

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Figure: Model fits

Summarizes the epidemic model fit with COVID-19 data for LAC from March 1 through 2021-03-01 for all disease states across multiple views: New cases, representing new daily incidence; the current number in a compartment at a specific date, relevant for understanding current prevalence rates and comparing with healthcare capacity limitations; and cumulative counts until a specific date. Observed data for available compartments are plotted as black dots.

  • New = new daily incidence
  • Current = current census in compartment
  • Cumulative = running total over time
  • Black dots depict COVID-19 data

Figures: Time-Varying Parameters

Reproductive Number \(R(t)\) and Effective Reproductive Number \(Reff(t)\)

Fraction of Observed Infections \(r(t)\)

\(\alpha(t)\), \(\kappa(t)\), \(\delta(t)\)

Time-varying CFR(t)

Time-varying IFR(t)

Figures: Compartmental Variables

Numbers infected

  • New = new daily incidence
  • Current = current census in compartment
  • Cumulative = running total over time
  • Black dots depict COVID-19 data

Current observed and total infections

New observed infections (with data)

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Current estimated total infections

Current observed infections

Current observed and total infections (together)

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Numbers in healthcare

  • New = new daily incidence
  • Current = current census in compartment
  • Cumulative = running total over time
  • Black dots depict COVID-19 data
  • Dotted black line marks healthcare capacity limits

Current in hospital and in ICU

New deaths

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Current in hospital

Current in ICU

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Risk model

\(\psi\) matrix - log conditional risks

\(\psi\) matrix edited

H.I V.H D.V
age_0.18 -2.00 -2.000 -2.00
age_19.49 0.00 0.000 0.00
age_50.64 0.95 0.950 0.95
age_65.79 1.90 1.900 1.90
age_80. 2.90 2.900 2.90
obese_0BMI.30 0.00 0.000 0.00
obese_1BMI30.40 0.60 0.049 0.11
obese_2BMI40. 1.20 0.098 0.23
smoker 0.57 0.480 0.67
comorbidity.yes 0.41 0.020 0.04

Risk probabilities by age

Figures show the mean, minimum, and maximum values of the probabilities of severe illness for each age group. The minimum and maximum indicate the range of values that can be taken on by the sub-profiles within each age group; for example for age group 65-79, a profile with low BMI, no smoking, and no comorbidities will have lower probabilites of severe illness than a profile with high BMI, smoking, and comorbidities.

P(H|I)

Probability of hospitalization given infection

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P(Q|H)

Probability of ICU admission given hospitalization

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P(D|Q)

Probability of death given ICU admission

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P(D|I)

Probability of death given infection

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Risk probability tables

P(H|I)

Probability of hospitalization given infection

P(Q|H)

Probability of ICU admission given hospitalization

P(D|Q)

Probability of death given ICU admission