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57 lines
2.1 KiB
57 lines
2.1 KiB
#' Retrieve National Surveillance of U.S. State and Local Public Health Laboratories Reporting to CDC
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#'
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#' @return data frame
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#' @references <https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/04102020/labs-regions.html>
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#' @export
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public_health_labs_national <- function() {
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xml2::read_html(
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"https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/04102020/labs-regions.html"
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) -> pg
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nat_tbl <- rvest::html_nodes(pg, xpath=".//table[contains(., 'National')]")
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nat_rows <- rvest::html_nodes(nat_tbl, "tbody > tr")
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lapply(nat_rows, function(.x) {
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nat_tds <- rvest::html_nodes(.x, "td")
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nat_tds <- gsub(",", "", rvest::html_text(nat_tds))
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as_tibble(as.data.frame(
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as.list(
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set_names(
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nat_tds, sprintf("X%02d", 1:length(nat_tds))
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)
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),
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stringsAsFactors = FALSE
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))
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}) -> nat_rows
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nat_tbl <- do.call(rbind.data.frame, nat_rows)
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total <- set_names(nat_tbl[, 1:5], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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total$age_group <- "Overall"
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a1 <- set_names(nat_tbl[, c(1:2, 6:8)], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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a1$age_group <- "0-4 yr"
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a2 <- set_names(nat_tbl[, c(1:2, 9:11)], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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a2$age_group <- "5-17 yr"
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a3 <- set_names(nat_tbl[, c(1:2, 12:14)], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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a3$age_group <- "18-49 yr"
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a4 <- set_names(nat_tbl[, c(1:2, 15:17)], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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a4$age_group <- "50-64 yr"
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a5 <- set_names(nat_tbl[, c(1:2, 18:20)], c("week", "num_labs", "tested", "tested_pos", "pct_pos"))
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a5$age_group <- "65+ yr"
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nat_tbl <- rbind(total, a1, a2, a3, a4, a5, stringsAsFactors = FALSE)
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nat_tbl$region <- "National"
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nat_tbl$source <- "Public Health Labs"
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nat_tbl$week <- clean_int(nat_tbl$week)
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nat_tbl$num_labs <- clean_int(nat_tbl$num_labs)
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nat_tbl$tested <- clean_int(nat_tbl$tested)
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nat_tbl$tested_pos <- clean_int(nat_tbl$tested_pos)
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nat_tbl$pct_pos <- clean_num(nat_tbl$pct_pos)/100
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nat_tbl[!is.na(nat_tbl$week),]
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}
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