get_p_Levin: Estimate Covid2019 outcome probabilities for a population...

In epicentre-msf/covidestim: Estimates Of Epidemiological Parameters For COVID19

Description

Estimate Covid19 outcome probabilities (death|infection), using age-severity estimates from Levin al. (2020), and the population age distribution for a given country, either taken from the UN World Population Prospects 2019 (WPP2019) or directly supplied by the user.

Usage

get_p_Levin(x, p_type = c("p_dead_inf"), p_stat = c("mean", "low_95",
  "up_95"), p_sex = c("total"))

Arguments

x	Either an ISO3 country code used to extract age-specific population estimates from the UN World Population Prospects 2019 dataset, or, a data.frame containing age categories in the first column and population counts (or proportions) in the second column
p_type	Outcome to estimate ("p_dead_inf" is the only option here)
p_stat	Statistic of the severity estimates to use (either "mean", "low_95", or "up_95")
p_sex	Use severity estimate for which sex. Can only be "total" here.

Value

Estimated outcome probability (scalar)

Author(s)

Anton Camacho

Patrick Barks <[e-mail]>

Flavio Finger <[e-mail]>

Source

Assessing the Age Specificity of Infection Fatality Rates for COVID-19: Systematic Review, Meta-Analysis, and Public Policy Implications Andrew T. Levin, William P. Hanage, Nana Owusu-Boaitey, Kensington B. Cochran, Seamus P. Walsh, Gideon Meyerowitz-Katz medRxiv 2020.07.23.20160895; doi: https://doi.org/10.1101/2020.07.23.20160895

Examples

# mean Pr(death|infection) for Canada (ISO3 code "CAN"), taking age
# distribution from WPP2019
get_p_Levin(x = "CAN", p_stat = "mean")

# use custom age-distribution
age_df <- data.frame(
  age = c("0-4", "5-9", "10-14", "15-19", "20-24", "25-29", "30-34", "35-39", "40-44", "45-49",
             "50-54", "55-59", "60-64", "65-69", "70-74", "75-79", "80-84", "85+"),
  pop = c(1023, 1720, 2422, 3456, 3866, 4104, 4003, 3576, 1210, 1023,
           1720, 2422, 3456, 3866, 4104, 4003, 3576, 1300),
  stringsAsFactors = FALSE
)

get_p_Levin(x = age_df, p_type = "p_dead_inf", p_stat = "mean", p_sex = "total")

epicentre-msf/covidestim documentation built on Jan. 1, 2021, 1:06 a.m.