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

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

Description

Estimate Covid19 outcome probabilities including hospitalizion|infection, ICU|hospitalization, death|hospitalization, and death|infection, using age-severity estimates from Salje et 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_Salje(x, p_type = c("p_hosp_inf", "p_icu_hosp", "p_dead_hosp",
  "p_dead_inf"), p_stat = c("mean", "low_95", "up_95"),
  p_sex = c("total", "male", "female"))

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 (either "p_hosp_inf", "p_icu_hosp", "p_dead_hosp", or "p_dead_inf")
p_stat	Statistic of the severity estimates to use (either "mean", "low_95", or "up_95")
p_sex	Use severity estimate for which sex (either "female", "male", or "total")

Value

Estimated outcome probability (scalar)

Author(s)

Anton Camacho

Patrick Barks <[e-mail]>

Source

Salje, H., Kiem, C.T., Lefrancq, N., Courtejoie, N., Bosetti, P., Paireau, J., Andronico, A., Hoze, N., Richet, J., Dubost, C.L., and Le Strat, Y. (2020) Estimating the burden of SARS-CoV-2 in France. Science. https://doi.org/10.1126/science.abc3517

Examples

# mean Pr(hospitalization|infection) for Canada (ISO3 code "CAN"), taking age
# distribution from WPP2019
get_p_Salje(x = "CAN", p_type = "p_hosp_inf", p_stat = "mean", p_sex = "total")

# use custom age-distribution
age_df <- data.frame(
  age = c("0-9", "10-19", "20-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80+"),
  pop = c(1023, 1720, 2422, 3456, 3866, 4104, 4003, 3576, 1210),
  stringsAsFactors = FALSE
)

get_p_Salje(x = age_df, p_type = "p_hosp_inf", p_stat = "mean", p_sex = "total")

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