scrape.R

# Purpose: retrieve human case data from the web
library(rvest)
library(data.table)
library(here)
uri <- "https://www.cdc.gov/bird-flu/situation-summary/index.html"

# read the html
page <- read_html(uri)

# extract the table
table <- html_table(page)

table_dt <- setDT(table[[1]])

table_dt_long <- melt(table_dt, id.vars = c("State"), variable.name = "Source", value.name = "Cases")

table_dt_long[, Cases := as.numeric(Cases)]
table_dt_long[, UpdateDTS := Sys.time()]

# write to disk
fwrite(table_dt_long, here("data-raw", "human_cases.csv"), append = TRUE)

# Get WW data

url <- "https://www.cdc.gov/wcms/vizdata/NCEZID_DIDRI/FluA/H5N1Table.json"
library(httr)
tmp <- tempfile()
httr::GET(url, write_disk(tmp))

dat <- jsonlite::fromJSON(tmp)

dat$UpdateDTS <- Sys.time()

dat_long <- dat |>
  tidyr::gather(DateDT, StatusDT, -Sewershed, -`State/Territory`, -County, -UpdateDTS)

fwrite(dat_long, here("data-raw", "ww_cases.csv"), append = TRUE)