get_p_Brazeau: 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 Brazeau 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_Brazeau(x, p_type = c("p_dead_inf", "p_dead_inf_serorev"),
  p_stat = c("mean", "low_95", "up_95"))

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" (default) or "p_dead_inf_serorev")
p_stat	Statistic of the severity estimates to use (either "mean", "low_95", or "up_95")

Value

Estimated outcome probability (scalar)

Author(s)

Anton Camacho

Patrick Barks <[e-mail]>

Flavio Finger <[e-mail]>

Source

Report 34: COVID-19 Infection Fatality Ratio: Estimates from Seroprevalence. Nicholas F Brazeau, Robert Verity, Sara Jenks, Han Fu, Charles Whittaker, Peter Winskill, Ilaria Dorigatti, Patrick Walker, Steven Riley, Ricardo P Schnekenberg, Henrique Hoeltgebaum, Thomas A Mellan, Swapnil Mishra, H Juliette T Unwin, Oliver J Watson, Zulma M Cucunubá, Marc Baguelin, Lilith Whittles, Samir Bhatt, Azra C Ghani, Neil M Ferguson, Lucy C Okell. https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-34-ifr/

Examples

# mean Pr(death|infection) for Canada (ISO3 code "CAN"), taking age
# distribution from WPP2019
get_p_Brazeau(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", "85-89", "90+"),
  pop = c(1023, 1720, 2422, 3456, 3866, 4104, 4003, 3576, 1210, 1023,
           1720, 2422, 3456, 3866, 4104, 4003, 3576, 1576, 854),
  stringsAsFactors = FALSE
)

get_p_Brazeau(x = age_df, p_type = "p_dead_inf", p_stat = "mean")

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