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

Description Usage Arguments Value Author(s) Source Examples

View source: R/get_p_ODriscoll.R

Description

Estimate Covid19 outcome probabilities (death|infection), using age-severity estimates from O'Driscoll 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

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get_p_ODriscoll(x, p_type = c("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 ("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 (either "female", "male", or "total")

Value

Estimated outcome probability (scalar)

Author(s)

Anton Camacho

Patrick Barks <patrick.barks@epicentre.msf.org>

Flavio Finger <flavio.finger@epicentre.msf.org>

Source

O’Driscoll, M., Dos Santos, G.R., Wang, L. et al. Age-specific mortality and immunity patterns of SARS-CoV-2. Nature (2020). https://doi.org/10.1038/s41586-020-2918-0

Examples

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

# 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+"),
  pop = c(1023, 1720, 2422, 3456, 3866, 4104, 4003, 3576, 1210, 1023,
           1720, 2422, 3456, 3866, 4104, 4003, 3576),
  stringsAsFactors = FALSE
)

get_p_ODriscoll(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.