mortality_rate_fun: Mortality rate
In EMDominic/SThelperfunctions: Helper Functions For Spatiotemporal Analysis

Description Usage Arguments Examples

View source: R/Functions.R

This function that takes in weekly or monthly aggreagated causes of deaths and population estimates then it computes mortality rates per 100 000 by country level and provincial level. This function takes output from the aggreagate_fun().

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mortality_rate_fun(df,
                   population_est,
                   scale.aggregate = c("Province", "Countrywide"))

`df`	Aggregated dataframe
`population_est`	Mid year population estimates. If by_province is TRUE, then provide provincial estimates else countrywide estimates.
`by_province`	Whether to aggregate by province or country level

## The function is currently defined as

mortality_rate_fun <- function(df,
                               population_est,
                               scale.aggregate = c("Province", "Countrywide")) {

  joint_df <- if (scale.aggregate == "Province")
  {left_join(df, population_est, by = c("DeathProv" = "Province", "Year"))}
  else {left_join(df, population_est,by = "Year")}

  joint_df %>%
    mutate(All_deaths_rate = (All_deaths/Pop_estimate)*100000,
           AllRes_deaths_rate = (AllRes_deaths/Pop_estimate)*100000,
           AllResU5_deaths_rate = (AllResU5_deaths/Pop_estimateU5)*100000,
           AllResG5_deaths_rate = (AllResG5_deaths/Pop_estimateG5)*100000,
           PI_deaths_rate = (PI_deaths/Pop_estimate)*100000,
           PIU5_deaths_rate = (PIU5_deaths/Pop_estimateU5)*100000,
           PIG5_deaths_rate = (PIG5_deaths/Pop_estimateG5)*100000,
           POther_deaths_rate = (POther_deaths/Pop_estimate)*100000,
           Flu_deaths_rate = (Flu_deaths/Pop_estimate)*100000,
           RSV_deaths_rate = (RSV_deaths/Pop_estimateU5)*100000)  %>%
    select(-c(All_deaths, AllRes_deaths, AllResU5_deaths, AllResG5_deaths, PI_deaths,
              PIU5_deaths, PIG5_deaths,
              POther_deaths, Flu_deaths, RSV_deaths, Year, Pop_estimate, Pop_estimateU5,
              Pop_estimateG5))
}