data-raw/irish_county_data.R

In curso-r/hamiltonCovid19: Hamilton Covid-19 Dashboard

## Update irish_county_data dataset

usethis::ui_todo("Checking update for irish_county_data dataset...")

`%>%` <- magrittr::`%>%`

url_irl <- "http://opendata-geohive.hub.arcgis.com/datasets/d9be85b30d7748b5b7c09450b8aede63_0.csv"

raw_irish_county_data <- tryCatch(
  read.csv(url_irl, stringsAsFactors = FALSE),
  error = function(x) NULL
)

if (is.null(raw_irish_county_data)) {
  usethis::ui_oops(paste0("Failed to connect to ", url_irl))
} else {

  # Testing new dataset
  old_irish_county_data <- readr::read_rds(
    "data-raw/rds/raw_irish_county_data.rds"
  )

  tab_duplicates <- raw_irish_county_data %>%
    dplyr::count(CountyName, TimeStamp) %>%
    dplyr::filter(n > 1)

  needed_columns <- c(
    "TimeStamp",
    "CountyName",
    "ConfirmedCovidCases",
    "PopulationProportionCovidCases",
    "ConfirmedCovidDeaths",
    "ConfirmedCovidRecovered"
  )

  missing_columns <- needed_columns[
    !needed_columns %in% names(raw_irish_county_data)
  ]

  if (nrow(old_irish_county_data) >= nrow(raw_irish_county_data)) {
    usethis::ui_done("Nothing to update in irish_county_data.")
  } else if (nrow(tab_duplicates) > 0) {
    usethis::ui_oops("New data has duplicated Date/CountyName entries. Dataset not updated.")
  } else if (length(missing_columns) > 0) {
    usethis::ui_oops(paste0(
      "The following columns are missing in the new dataset: ",
      paste(missing_columns, collapse = ", "),
      ". Dataset not updated."
    ))
  } else {
    # Updating dataset
    suppressMessages({
      readr::write_rds(
        raw_irish_county_data,
        "data-raw/rds/raw_irish_county_data.rds",
        compress = "xz"
      )

      geo_irish_county <- sf::st_read(
        "data-raw/geojson/counties_simple.geojson",
        quiet =TRUE
      )

      irish_county_data <- raw_irish_county_data %>%
        dplyr::mutate(Date = as.Date(TimeStamp)) %>%
        dplyr::arrange(Date, CountyName) %>%
        dplyr::group_by(CountyName) %>%
        dplyr::mutate(DailyCases = c(0, diff(ConfirmedCovidCases))) %>%
        dplyr::mutate(
          last14per100k_raw = RcppRoll::roll_sum(
            DailyCases,
            14,
            align = "right",
            fill = 0
          ),
          last14per100k = 1e5 * last14per100k_raw / PopulationCensus16,
        ) %>%
        dplyr::ungroup() %>%
        dplyr::left_join(
          geo_irish_county,
          by = c("CountyName" = "NAME_TAG")
        ) %>%
        sf::st_as_sf() %>%
        dplyr::select(
          Date,
          CountyName,
          ConfirmedCovidCases:ConfirmedCovidRecovered,
          last14per100k,
          LATITUDE, LONGITUDE,
          geometry
        )

      deploy_app <- TRUE

      usethis::use_data(irish_county_data, overwrite = TRUE)
    })
    usethis::ui_done("irish_county_data dataset updated!")
  }
}