You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

87 lines
3.1 KiB

#' Retrieve CDC flu data
#' Uses the data source from the CDC FluView \url{}
#' and provides flu reporting data as either a single data frame or a list
#' of data frames (depending on whether either WHO NREVSS or ILINet - or both - is chosen)
#' @param region one of "\code{hhs}", "\code{census}", "\code{national}"
#' @param sub_region depends on the \code{region_type}.\cr
#' For "\code{national}", the \code{sub_region} should be \code{NA}.\cr
#' For "\code{hhs}", should be a vector between \code{1:10}.\cr
#' For "\code{census}", should be a vector between \code{1:9}
#' @param data_source either of "\code{who}" (for WHO NREVSS) or "\code{ilinet}" or "\code{all}" (for both)
#' @param years a vector of years to retrieve data for (i.e. \code{2014} for CDC flu season 2014-2015)
#' @return If only a single \code{data_source} is specified, then a single \code{data.frame} is
#' returned, otherwise a named list with each \code{data.frame} is returned.
#' @export
#' @examples \dontrun{
#' flu <- get_flu_data("hhs", 1:10, c("who", "ilinet"), years=2000:2014)
#' }
get_flu_data <- function(region="hhs", sub_region=1:10,
data_source="ilinet", years=2014) {
region <- tolower(region)
data_source <- tolower(data_source)
if (!(region %in% c("hhs", "census", "national")))
stop("Error: region must be one of hhs, census or national")
if (length(region) != 1)
stop("Error: can only select one region")
if (region=="national") sub_region = ""
if ((region=="hhs") && !all(sub_region %in% 1:10))
stop("Error: sub_region values must fall between 1:10 when region is 'hhs'")
if ((region=="census") && !all(sub_region %in% 1:19))
stop("Error: sub_region values must fall between 1:10 when region is 'census'")
if (!all(data_source %in% c("who", "ilinet")))
stop("Error: data_source must be either 'who', 'ilinet' or both")
if (any(years < 1997))
stop("Error: years should be > 1997")
years <- years - 1960
reg <- as.numeric(c("hhs"=1, "census"=2, "national"=3)[[region]])
data_source <- gsub("who", "WHO_NREVSS", data_source)
data_source <- gsub("ilinet", "ILINet", data_source)
params <- list(SubRegionsList=paste0(sub_region, collapse=","),
SeasonsList=paste0(years, collapse=","))
out_file <- tempfile(fileext=".zip")
tmp <- POST("",
if (!(file.exists(out_file)))
stop("Error: cannot process downloaded data")
out_dir <- tempdir()
files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
file_list <- pblapply(files, function(x) {
ct <- ifelse(grepl("who", x,, 0, 1)
read.csv(x, header=TRUE, skip=ct, stringsAsFactors=FALSE)
names(file_list) <- substr(basename(files), 1, 3)
if (length(file_list) == 1) {
} else {