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62 lines
2.5 KiB
62 lines
2.5 KiB
#' Retrieve Provisional Death Counts for Coronavirus Disease (COVID-19)
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#'
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#' @note Please see the indicated reference for all the caveats and precise meanings for each field. Also,
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#' this function used the JSON API (<https://data.cdc.gov/resource/hc4f-j6nb.json>)
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#' @return a list with 4 named elements: `by_week`, `by_age`, `by_state`, `by_sex`
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#' @references <https://data.cdc.gov/api/views/hc4f-j6nb/rows.csv?accessType=DOWNLOAD&bom=true&format=true>
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#' @export
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provisional_death_counts <- function() {
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res <- jsonlite::fromJSON("https://data.cdc.gov/resource/hc4f-j6nb.json")
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res <- as_tibble(res)
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res$covid_deaths <- clean_int(res$covid_deaths)
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res$total_deaths <- clean_int(res$total_deaths)
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res$pneumonia_deaths <- clean_int(res$pneumonia_deaths)
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res$pneumonia_and_covid_deaths <- clean_int(res$pneumonia_and_covid_deaths)
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res$all_influenza_deaths_j09_j11 <- clean_int(res$all_influenza_deaths_j09_j11)
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res$percent_expected_deaths <- clean_num(res$percent_expected_deaths)
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by_week <- res[res$group == "By week",]
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by_age <- res[res$group == "By age",]
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by_state <- res[res$group == "By state",]
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by_sex <- res[res$group == "By sex",]
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by_week <- by_week[!grepl("total", tolower(by_week$indicator)),]
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by_week$group <- NULL
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by_week$indicator <- as.Date(by_week$indicator, "%m/%d/%Y")
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colnames(by_week) <- c(
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"week", "covid_deaths", "total_deaths", "percent_expected_deaths",
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"pneumonia_deaths", "pneumonia_and_covid_deaths", "all_influenza_deaths_j09_j11"
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)
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by_age$group <- NULL
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colnames(by_age) <- c(
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"age_group", "covid_deaths", "total_deaths", "percent_expected_deaths",
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"pneumonia_deaths", "pneumonia_and_covid_deaths", "all_influenza_deaths_j09_j11"
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)
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by_age$age_group <- sub("–", "-", by_age$age_group, fixed=TRUE)
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by_age$age_group <- sub("yea.*", "yr", by_age$age_group)
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by_state$group <- NULL
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colnames(by_state) <- c(
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"state", "covid_deaths", "total_deaths", "percent_expected_deaths",
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"pneumonia_deaths", "pneumonia_and_covid_deaths", "all_influenza_deaths_j09_j11"
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)
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by_state <- by_state[by_state$state != "Total US",]
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by_sex$group <- NULL
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colnames(by_sex) <- c(
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"sex", "covid_deaths", "total_deaths", "percent_expected_deaths",
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"pneumonia_deaths", "pneumonia_and_covid_deaths", "all_influenza_deaths_j09_j11"
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)
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by_sex <- by_sex[!grepl("Total", by_sex$sex),]
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list(
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by_week = as_tibble(by_week),
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by_age = as_tibble(by_age),
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by_state = as_tibble(by_state),
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by_sex = as_tibble(by_sex)
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)
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}
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