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Directly standardized incidence rates using the WHO standard population

Source: R/incidencR.R
incidencR.Rd

Directly standardized incidence rates inspired by the dsr package by Matt Kumar. The incidence rates are standardized on 5-year age intervals and sex for each year in the period 1990-2025 based on population tables of the Danish population. Lastly the incidence rates are weighted based on the WHO world population.

Usage

incidencR(
  data,
  group,
  strata = list(c("year")),
  unit = 1e+05,
  ci.method = "lognormal",
  reference = "full",
  index,
  age = age,
  sex = sex
)

Arguments

data

data set containing age, sex and index date and group

group

optional if incidence rates should be provided per group

strata

list of vectors for which strata the incidence rates should be reported (e.g. per age-group and sex)

ci.method

the method for derivation of confidence intervals. Default is "normal". If negative CIs are reported, use "lognormal"

reference

whether the reference population should include all possible age-sex-groups ("full" (default)) or only the age-groups present in data ("partial")

index

variable name of the index data

age

name of the age variable

sex

name of the sex variable

pyears

the unit of the incidence rate. Default is 100.000 person years

Value

a standardized incidence rate of the overall population and, if specified in the strata-argument, stratified incidence rates

Examples

(rates <-
incidencR(redcap_df %>%
           recodR(list("sex" = list("Female" = 1,
                                     "Male" = 2))),
          index = date_of_surgery,
          group = type,
          unit = 100000,
          strata = list(c("year"),
                        c("age", "sex"),
                        c("year", "type"),
                        c("year", "type", "age"),
                        c("type", "age"),
                        c("year", "age", "sex", "type"))))
#> Error in mutate(., age_group = ifelse(age_group == "85-150", "85+", as.character(age_group)),     `:=`(!!sym(group_c), as.character(!!sym(group_c)))): ℹ In argument: `age_group = ifelse(age_group == "85-150", "85+",
#>   as.character(age_group))`.
#> Caused by error:
#> ! object 'age_group' not found

ggplot(rates$year_type, aes(x=year, y=weighted_rate, color = type, fill = type)) +
  geom_point() +
  geom_line() +
  #geom_ribbon(aes(ymin = weighted_lower, ymax = weighted_upper), alpha = 0.2, color = NA) +
  geom_smooth(se=F) +
  theme_classic()
#> Error: object 'rates' not found