#' Retrieves state, regional or national influenza statistics from the CDC #' #' Uses the data source from the #' \href{http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}{CDC FluView} #' and provides flu reporting data as either a single data frame or a list of #' data frames (depending on whether either \code{WHO NREVSS} or \code{ILINet} #' (or both) is chosen. #' #' A lookup table between HHS regions and their member states/territories #' is provided in \code{\link{hhs_regions}}. #' #' @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). Default value is the current year and all #' \code{years} values should be > \code{1997} #' @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. #' @note There is often a noticeable delay when making the API request to the CDC. #' This is not due to a large download size, but the time it takes for their #' servers to crunch the data. Wrap the function call in \code{httr::with_verbose} #' if you would like to see what's going on. #' @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=as.numeric(format(Sys.Date(), "%Y"))) { 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", "all"))) stop("Error: data_source must be either 'who', 'ilinet', 'all' or c('who', 'ilinet')") if (any(years < 1997)) stop("Error: years should be > 1997") # format the input parameters to fit the CDC API years <- years - 1960 reg <- as.numeric(c("hhs"=1, "census"=2, "national"=3)[[region]]) if ("all" %in% data_source) data_source <- c("who", "ilinet") data_source <- gsub("who", "WHO_NREVSS", data_source) data_source <- gsub("ilinet", "ILINet", data_source) params <- list(SubRegionsList=paste0(sub_region, collapse=","), DataSources=paste0(data_source, collapse=","), RegionID=reg, SeasonsList=paste0(years, collapse=",")) out_file <- tempfile(fileext=".zip") tmp <- httr::POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase2CustomDownload.ashx", body=params, write_disk(out_file)) stop_for_status(tmp) if (!(file.exists(out_file))) stop("Error: cannot process downloaded data") out_dir <- tempdir() files <- unzip(out_file, exdir=out_dir, overwrite=TRUE) pb <- dplyr::progress_estimated(length(files)) purrr::map(files, function(x) { pb$tick()$print() ct <- ifelse(grepl("who", x, ignore.case=TRUE), 1, 1) suppressMessages(readr::read_csv(x, skip=ct)) }) -> file_list names(file_list) <- substr(basename(files), 1, 3) if (length(file_list) == 1) { return(file_list[[1]]) } else { return(file_list) } }