data-raw/burden.R

In QuartzSoftwareLLC/shiny.fluToolKit: What the Package Does (One Line, Title Case)

library(dplyr)
source("data-raw/helpers.R")

raw <- read.csv(url("https://s3.amazonaws.com/quartzdata/datasets/influenza-burden.csv"))

raw %>%
  subset(age_group != "All ages") -> tmp

# save 0-4 and 5-17 to later be re added
tmp %>% 
  subset(age_group %in% c("0-4 yrs", "5-17 yrs")) -> saved_age_groups

tmp %>%
  mutate(
    age_group = recode_factor(age_group,
      "0-4 yrs" = "0 - 17",
      "5-17 yrs" = "0 - 17",
      "18-49 yrs" = "18 - 49",
      "50-64 yrs" = "50 - 64",
      "65+ yrs" = "65+"
    )
  ) %>%
  rbind(saved_age_groups) %>%
  group_by(age_group, season, measure) %>%
  summarise_at(c("ci_lower", "ci_upper", "value"), sum, na.rm = TRUE) %>%
  ungroup() %>%
  mutate(rate = grepl("*rate", measure)) %>%
    rename(upper_ci = "ci_upper", lower_ci = "ci_lower") %>%
    select(c(required_columns, measure, rate)) -> burden


usethis::use_data(burden,
  overwrite = T
)