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95 lines
3.4 KiB
95 lines
3.4 KiB
#' Retrieve ILINet Surveillance Data
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#'
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#' The CDC FluView Portal provides in-season and past seasons' national, regional,
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#' and state-level outpatient illness and viral surveillance data from both
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#' ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
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#' (National Respiratory and Enteric Virus Surveillance System).
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#'
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#' This function retrieves current and historical ILINet surveillance data for
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#' the identified region.
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#'
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#' @md
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#' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
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#' @references
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#' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
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#' - [ILINet Portal](https://wwwn.cdc.gov/ilinet/) (Login required)
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#' - [WHO/NREVSS](https://www.cdc.gov/surveillance/nrevss/index.html)
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#' @export
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#' @examples
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#' national_ili <- ilinet("national")
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#' hhs_ili <- ilinet("hhs")
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#' census_ili <- ilinet("census")
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#' state_ili <- ilinet("state")
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#' \dontrun{
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#' library(purrr)
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#' map_df(
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#' c("national", "hhs", "census", "state"),
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#' ~ilinet(.x) %>% readr::type_convert())
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#' }
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ilinet <- function(region=c("national", "hhs", "census", "state")) {
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region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
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list(
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AppVersion = "Public",
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DatasourceDT = list(list(ID = 1, Name = "ILINet")),
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RegionTypeId = .region_map[region]
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) -> params
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params$SubRegionsDT <- switch(region,
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national = { list(list(ID=0, Name="")) },
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hhs = { lapply(1:10, function(i) list(ID=i, Name=as.character(i))) },
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census = { lapply(1:9, function(i) list(ID=i, Name=as.character(i))) },
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state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
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)
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seasons <- 37:((unclass(as.POSIXlt(Sys.time()))[["year"]] + 1900) - 1960)
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params$SeasonsDT <- lapply(seasons, function(i) list(ID=i, Name=as.character(i)))
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tf <- tempfile(fileext = ".zip")
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td <- tempdir()
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on.exit(unlink(tf), TRUE)
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httr::POST(
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url = "https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload",
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httr::user_agent(.cdcfluview_ua),
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httr::add_headers(
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Origin = "https://gis.cdc.gov",
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Accept = "application/json, text/plain, */*",
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Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
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),
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encode = "json",
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body = params,
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# httr::verbose(),
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httr::write_disk(tf)
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) -> res
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httr::stop_for_status(res)
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nm <- unzip(tf, overwrite = TRUE, exdir = td)
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xdf <- read.csv(nm, skip = 1, stringsAsFactors=FALSE)
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xdf <- .mcga(xdf)
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suppressWarnings(xdf$weighted_ili <- to_num(xdf$weighted_ili))
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suppressWarnings(xdf$unweighted_ili <- to_num(xdf$unweighted_ili))
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suppressWarnings(xdf$age_0_4 <- to_num(xdf$age_0_4))
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suppressWarnings(xdf$age_25_49 <- to_num(xdf$age_25_49))
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suppressWarnings(xdf$age_25_64 <- to_num(xdf$age_25_64))
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suppressWarnings(xdf$age_5_24 <- to_num(xdf$age_5_24))
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suppressWarnings(xdf$age_50_64 <- to_num(xdf$age_50_64))
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suppressWarnings(xdf$age_65 <- to_num(xdf$age_65))
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suppressWarnings(xdf$ilitotal <- to_num(xdf$ilitotal))
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suppressWarnings(xdf$num_of_providers <- to_num(xdf$num_of_providers))
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suppressWarnings(xdf$total_patients <- to_num(xdf$total_patients))
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suppressWarnings(xdf$week_start <- as.Date(sprintf("%s-%02d-1", xdf$year, xdf$week), "%Y-%U-%u"))
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if (region == "national") xdf$region <- "National"
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if (region == "hhs") xdf$region <- factor(xdf$region, levels=sprintf("Region %s", 1:10))
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class(xdf) <- c("tbl_df", "tbl", "data.frame")
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xdf
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}
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