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#' 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.\cr\cr
#' **ALSO** The new CDC API seems to be missing some public health lab data fields.
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#' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
#' @param years a vector of years to retrieve data for (i.e. `2014` for CDC
#' flu season 2014-2015). CDC has data for this API going back to 1997.
#' Default value (`NULL`) means retrieve **all** years. NOTE: if you
#' happen to specify a 2-digit season value (i.e. `57` == 2017-2018)
#' the function is smart enough to retrieve by season ID vs convert that
#' to a year.
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#' @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{
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#' 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"), years=NULL) {
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region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
meta <- jsonlite::fromJSON("https://gis.cdc.gov/grasp/flu2/GetPhase02InitApp?appVersion=Public")
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list(
AppVersion = "Public",
DatasourceDT = list(list(ID = 1, Name = "WHO_NREVSS")),
RegionTypeId = .region_map[region]
) -> params
params$SubRegionsDT <- switch(
region,
national = { list(list(ID=0, Name="")) },
hhs = { lapply(1:10, function(i) list(ID=i, Name=as.character(i))) },
census = { lapply(1:9, function(i) list(ID=i, Name=as.character(i))) },
state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
)
available_seasons <- sort(meta$seasons$seasonid)
if (is.null(years)) { # ALL YEARS
years <- available_seasons
} else { # specified years or seasons or a mix
years <- as.numeric(years)
years <- ifelse(years > 1996, years - 1960, years)
years <- sort(unique(years))
years <- years[years %in% available_seasons]
if (length(years) == 0) {
years <- rev(sort(meta$seasons$seasonid))[1]
curr_season_descr <- meta$seasons[meta$seasons$seasonid == years, "description"]
message(sprintf("No valid years specified, defaulting to this flu season => ID: %s [%s]",
years, curr_season_descr))
}
}
params$SeasonsDT <- lapply(years, function(i) list(ID=i, Name=as.character(i)))
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tf <- tempfile(fileext = ".zip")
td <- tempdir()
on.exit(unlink(tf), TRUE)
httr::POST(
url = "https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload",
httr::user_agent(.cdcfluview_ua),
httr::add_headers(
Origin = "https://gis.cdc.gov",
Accept = "application/json, text/plain, */*",
Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
),
encode = "json",
body = params,
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# httr::verbose(),
httr::timeout(.httr_timeout),
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httr::write_disk(tf)
) -> res
httr::stop_for_status(res)
nm <- unzip(tf, overwrite = TRUE, exdir = td)
lapply(nm, function(x) {
tdf <- read.csv(x, skip = 1, stringsAsFactors=FALSE)
tdf <- .mcga(tdf)
class(tdf) <- c("tbl_df", "tbl", "data.frame")
tdf[tdf=="X"] <- NA
tdf[tdf=="XX"] <- NA
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tdf
}) -> xdf
xdf <- setNames(xdf, sub("who_nrevss_", "", tools::file_path_sans_ext(tolower(basename(nm)))))
xdf <- lapply(xdf, function(.x) {
x_cols <- colnames(.x)
if ((("year" %in% x_cols) & ("week" %in% x_cols))) {
.x$wk_date <- suppressWarnings(mmwr_week_to_date(.x$year, .x$week))
} else {
.x$wk_date <- as.Date(NA)
}
if (region == "national") .x$region <- "National"
.x
})
xdf
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}