data-raw/ve.R

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

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

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

raw %>% mutate(
    adjusted_ve_percent = replace(adjusted_ve_percent, adjusted_ve_percent=="NR", 0),
    across(c(adjusted_ve_percent_upper_ci, adjusted_ve_percent_lower_ci, adjusted_ve_percent), as.numeric),
    age_group = recode_factor(age_group,
      "6 mos-17" = "0 - 17",
      "18-49" = "18 - 49",
      "50-64" = "50 - 64",
      "over 65" = "65+"
    )
  ) %>%
  rename(value = "adjusted_ve_percent",
         lower_ci = "adjusted_ve_percent_lower_ci",
         upper_ci = "adjusted_ve_percent_upper_ci",
  ) %>%
  select(c(required_columns, strain)) -> ve

ve_strains <- unique_sort(ve$strain)

usethis::use_data(
  ve_strains,
  ve,
  overwrite = T
)