/
seir_params.yaml
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/
seir_params.yaml
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###############################################################
#
# These are parameters for a discrete time model implementation of
# a susceptible-exposed-infective-recovered (SEIR)
# epidemiological model. These parameters are for variants of
# COVID-19.
#
###############################################################
- name: Baseline variant
start date: {year: 2020, month: 1, day: 1}
R0:
1st infection: 2.25
Reinfection: 1.9
k factor: 0.1
unobserved fraction of cases:
first infection: 0.47
reinfection: 0.47
population at risk fraction: 0.05 # As a fraction of total population
case fatality rate among 1st infections:
average: 0.011
at risk: 0.073
overflow hospitalized mortality rate factor: 2
fraction of observed cases among 1st infections requiring hospitalization:
average: 0.031
at risk: 0.108
case fatality rate among reinfections:
average: 0.008
at risk: 0.033
fraction of observed reinfection cases requiring hospitalization:
average: 0.021
at risk: 0.060
transitioning rates:
prob infected given exposed: [0,0.025,0.1,0.2,0.3,0.4,0.4,0.4,0.4,0.4,0.4,0.4]
prob recover or death given infected: [0,0,0,0,0.05,0.05,0.06,0.06,0.06,0.07,0.07,
0.08,0.08,0.09,0.08,0.09,0.1,0.11,
0.12,0.13,0.15,0.18,0.22,0.29,0.06,
0.07,0.07,0.08,0.08,0.09,0.1,0.11]
prob reinfected given reexposed: [0,0.11,0.22,0.29,0.34,0.38,0.41,0.45,0.51,0.61]
prob recovery or death given reinfected: [0.00,0.00,0.13,0.13,0.19,0.19,0.16,0.16,
0.16,0.16,0.16,0.19,0.19,0.19,0.19,0.19,
0.30,0.30,0.30,0.30,0.30]
recovery rate for at risk as fraction of not at risk: 0.75
recovery rate for at risk as fraction of not at risk among reinfected: 1.0
protective efficacy of previous infection or inocculation: # points of interpolation given by month since infection/inocculation
- [{month: 0}, 0.9]
- [{month: 4}, 0.9] #
statistical-model:
coeff of variation of infected where spreading: 0.6
initial:
infected fraction:
Ports of entry: 0.0001 # As a fraction of total population
Other provinces: 0.00005
proportion of global infection rate:
- [{year: 2020, month: 1, day: 1}, 1]
- [{year: 2020, month: 3, day: 20}, 1]
- [{year: 2020, month: 4, day: 7}, 1]
- [{year: 2020, month: 5, day: 19}, 1]
- [{year: 2020, month: 7, day: 30}, 1]
- [{year: 2020, month: 10, day: 6}, 1]
- [{year: 2020, month: 11, day: 16}, 1]
- [{year: 2021, month: 4, day: 11}, 0.992]
- [{year: 2021, month: 5, day: 2}, 0.975]
- [{year: 2021, month: 5, day: 30}, 0.862]
- [{year: 2021, month: 6, day: 27}, 0.533]
- [{year: 2021, month: 7, day: 18}, 0.294]
- [{year: 2021, month: 8, day: 01}, 0.179]
- [{year: 2021, month: 9, day: 29}, 0.08]
- [{year: 2021, month: 10, day: 10}, 0.042]
- name: Delta variant
start date: {year: 2021, month: 3, day: 1}
R0:
1st infection: 6.4
Reinfection: 1.9
k factor: 0.1
unobserved fraction of cases:
first infection: 0.47
reinfection: 0.47
population at risk fraction: 0.05 # As a fraction of total population
case fatality rate among 1st infections:
average: 0.010
at risk: 0.069
overflow hospitalized mortality rate factor: 2
fraction of observed cases among 1st infections requiring hospitalization:
average: 0.030
at risk: 0.103
case fatality rate among reinfections:
average: 0.008
at risk: 0.033
fraction of observed reinfection cases requiring hospitalization:
average: 0.021
at risk: 0.060
transitioning rates:
prob infected given exposed: [0,0.11,0.22,0.29,0.34,0.38,0.41,0.45,0.51,0.61]
prob recover or death given infected: [0.00,0.00,0.00,0.00,0.00,0.00,0.06,0.06,
0.05,0.05,0.05,0.20,0.20,0.20,0.20,0.20,
0.13,0.13,0.13,0.13,0.13]
prob reinfected given reexposed: [0,0.11,0.22,0.29,0.34,0.38,0.41,0.45,0.51,0.61]
prob recovery or death given reinfected: [0.00,0.00,0.00,0.00,0.00,0.00,0.06,0.06,
0.05,0.05,0.05,0.20,0.20,0.20,0.20,0.20,
0.13,0.13,0.13,0.13,0.13]
recovery rate for at risk as fraction of not at risk: 0.75
recovery rate for at risk as fraction of not at risk among reinfected: 1.0
protective efficacy of previous infection or inocculation: # points of interpolation given by month since infection/inocculation
- [{month: 0}, 0.93]
- [{month: 4}, 0.53]
statistical-model:
coeff of variation of infected where spreading: 0.6
initial: # at variant's start date
infected fraction:
Ports of entry: 0.0001 # As a fraction of total population
Other provinces: 0
proportion of global infection rate:
- [{year: 2020, month: 1, day: 1}, 0.0000]
- [{year: 2020, month: 3, day: 20}, 0.0000]
- [{year: 2020, month: 4, day: 7}, 0.0000]
- [{year: 2020, month: 5, day: 19}, 0.0000]
- [{year: 2020, month: 7, day: 30}, 0.0000]
- [{year: 2020, month: 10, day: 6}, 0.0000]
- [{year: 2020, month: 11, day: 16}, 0.0000]
- [{year: 2021, month: 4, day: 11}, 0.008]
- [{year: 2021, month: 5, day: 2}, 0.025]
- [{year: 2021, month: 5, day: 30}, 0.138]
- [{year: 2021, month: 6, day: 27}, 0.467]
- [{year: 2021, month: 7, day: 18}, 0.706]
- [{year: 2021, month: 8, day: 01}, 0.821]
- [{year: 2021, month: 9, day: 29}, 0.92]
- [{year: 2021, month: 10, day: 10}, 0.958]