|
|
|
|
#' Retrieve WHO/NREVSS Surveillance Data
|
|
|
|
|
#'
|
|
|
|
|
#' The CDC FluView Portal provides in-season and past seasons' national, regional,
|
|
|
|
|
#' and state-level outpatient illness and viral surveillance data from both
|
|
|
|
|
#' ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
|
|
|
|
|
#' (National Respiratory and Enteric Virus Surveillance System).
|
|
|
|
|
#'
|
|
|
|
|
#' This function retrieves current and historical WHO/NREVSS surveillance data for
|
|
|
|
|
#' the identified region.
|
|
|
|
|
#'
|
|
|
|
|
#' @md
|
|
|
|
|
#' @note HHS, Census and State data retrieval is not as "instantaneous" as their ILINet
|
|
|
|
|
#' counterparts.\cr\cr
|
|
|
|
|
#' Also, beginning for the 2015-16 season, reports from public health and clinical
|
|
|
|
|
#' laboratories are presented separately in the weekly influenza update. This is
|
|
|
|
|
#' the reason why a list of data frames is returned.
|
|
|
|
|
#' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
|
|
|
|
|
#' @return list of data frames identified by
|
|
|
|
|
#' - `combined_prior_to_2015_16`
|
|
|
|
|
#' - `public_health_labs`
|
|
|
|
|
#' - `clinical_labs`
|
|
|
|
|
#' @references
|
|
|
|
|
#' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
|
|
|
|
|
#' - [ILINet Portal](https://wwwn.cdc.gov/ilinet/) (Login required)
|
|
|
|
|
#' - [WHO/NREVSS](https://www.cdc.gov/surveillance/nrevss/index.html)
|
|
|
|
|
#' @export
|
|
|
|
|
#' @examples \dontrun{
|
|
|
|
|
#' national_who <- who_nrevss("national")
|
|
|
|
|
#' hhs_who <- who_nrevss("hhs")
|
|
|
|
|
#' census_who <- who_nrevss("census")
|
|
|
|
|
#' state_who <- who_nrevss("state")
|
|
|
|
|
#' }
|
|
|
|
|
who_nrevss <- function(region=c("national", "hhs", "census", "state")) {
|
|
|
|
|
|
|
|
|
|
region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
|
|
|
|
|
|
|
|
|
|
list(
|
|
|
|
|
AppVersion = "Public",
|
|
|
|
|
DatasourceDT = list(list(ID = 1, Name = "WHO_NREVSS")),
|
|
|
|
|
RegionTypeId = .region_map[region]
|
|
|
|
|
) -> params
|
|
|
|
|
|
|
|
|
|
params$SubRegionsDT <- switch(
|
|
|
|
|
region,
|
|
|
|
|
national = { list(list(ID=0, Name="")) },
|
|
|
|
|
hhs = { lapply(1:10, function(i) list(ID=i, Name=as.character(i))) },
|
|
|
|
|
census = { lapply(1:9, function(i) list(ID=i, Name=as.character(i))) },
|
|
|
|
|
state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
|
|
|
|
|
)
|
|
|
|
|
|
|
|
|
|
seasons <- 37:((unclass(as.POSIXlt(Sys.time()))[["year"]] + 1900) - 1960)
|
|
|
|
|
params$SeasonsDT <- lapply(seasons, function(i) list(ID=i, Name=as.character(i)))
|
|
|
|
|
|
|
|
|
|
tf <- tempfile(fileext = ".zip")
|
|
|
|
|
td <- tempdir()
|
|
|
|
|
|
|
|
|
|
on.exit(unlink(tf), TRUE)
|
|
|
|
|
|
|
|
|
|
httr::POST(
|
|
|
|
|
url = "https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload",
|
|
|
|
|
httr::user_agent(.cdcfluview_ua),
|
|
|
|
|
httr::add_headers(
|
|
|
|
|
Origin = "https://gis.cdc.gov",
|
|
|
|
|
Accept = "application/json, text/plain, */*",
|
|
|
|
|
Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
|
|
|
|
|
),
|
|
|
|
|
encode = "json",
|
|
|
|
|
body = params,
|
|
|
|
|
httr::verbose(),
|
|
|
|
|
httr::timeout(60),
|
|
|
|
|
httr::write_disk(tf)
|
|
|
|
|
) -> res
|
|
|
|
|
|
|
|
|
|
httr::stop_for_status(res)
|
|
|
|
|
|
|
|
|
|
nm <- unzip(tf, overwrite = TRUE, exdir = td)
|
|
|
|
|
|
|
|
|
|
lapply(nm, function(x) {
|
|
|
|
|
|
|
|
|
|
tdf <- read.csv(x, skip = 1, stringsAsFactors=FALSE)
|
|
|
|
|
tdf <- .mcga(tdf)
|
|
|
|
|
class(tdf) <- c("tbl_df", "tbl", "data.frame")
|
|
|
|
|
|
|
|
|
|
tdf[tdf=="X"] <- NA
|
|
|
|
|
|
|
|
|
|
tdf
|
|
|
|
|
|
|
|
|
|
}) -> xdf
|
|
|
|
|
|
|
|
|
|
setNames(xdf, sub("who_nrevss_", "", tools::file_path_sans_ext(tolower(basename(nm)))))
|
|
|
|
|
|
|
|
|
|
}
|
