diff --git a/DESCRIPTION b/DESCRIPTION index 4b41a40..960ad58 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,8 +3,8 @@ Type: Package Title: Retrieve U.S. Flu Season Data from the CDC FluView Portal Version: 0.5.2 Date: 2017-03-14 -Author: Bob Rudis (bob@rud.is) -Maintainer: Bob Rudis +Authors@R: c(person("Bob","Rudis", email = "bob@rud.is", role = c("aut", "cre")), + person("Craig", "McGowan", email = "mcgowan.cj@gmail.com", role = "ctb")) Encoding: UTF-8 Description: The U.S. Centers for Disease Control (CDC) maintains a portal for diff --git a/R/get_flu_data.r b/R/get_flu_data.r index 22d4279..71dbb39 100644 --- a/R/get_flu_data.r +++ b/R/get_flu_data.r @@ -9,11 +9,14 @@ #' 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 region one of "\code{hhs}", "\code{census}", "\code{national}", +#' "\code{state}" #' @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} +#' For "\code{census}", should be a vector between \code{1:9}.\cr +#' For "\code{state}", should be a vector of state/territory names +#' or "\code{all}". #' @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 @@ -37,13 +40,13 @@ get_flu_data <- function(region="hhs", sub_region=1:10, region <- tolower(region) data_source <- tolower(data_source) - if (!(region %in% c("hhs", "census", "national"))) + if (!(region %in% c("hhs", "census", "national", "state"))) 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=="national") sub_region = 0 if ((region=="hhs") && !all(sub_region %in% 1:10)) stop("Error: sub_region values must fall between 1:10 when region is 'hhs'") @@ -57,31 +60,75 @@ get_flu_data <- function(region="hhs", sub_region=1:10, if (any(years < 1997)) stop("Error: years should be > 1997") - # format the input parameters to fit the CDC API - - years <- years - 1960 + # Match names of states to numbers for API + if (region == "state") { + sub_region <- tolower(sub_region) - reg <- as.numeric(c("hhs"=1, "census"=2, "national"=3)[[region]]) + if (any(sub_region == "all")) { + sub_region_inpt <- 1:57 + } else { + state_match <- data.frame(state = tolower(c(sort(c(datasets::state.name, + "District of Columbia")), + "American Samoa", + "Commonwealth of the Northern Mariana Islands", + "Puerto Rico", + "Virgin Islands", + "New York City", + "Los Angeles")), + num = 1:57, + stringsAsFactors = F) + + sub_region_inpt <- state_match$num[state_match$state %in% sub_region] + + if (length(sub_region_inpt) == 0) + stop("Error: no eligible state/territory names provided") + } + } else sub_region_inpt <- sub_region - if ("all" %in% data_source) data_source <- c("who", "ilinet") + # format the input parameters to fit the CDC API - data_source <- gsub("who", "WHO_NREVSS", data_source) - data_source <- gsub("ilinet", "ILINet", data_source) + years <- years - 1960 - params <- list(SubRegionsList = paste0(sub_region, collapse=","), - DataSources = paste0(data_source, collapse=","), - RegionID = reg, - SeasonsList = paste0(years, collapse=",")) + reg <- as.numeric(c("hhs"=1, "census"=2, "national"=3, "state" = 5)[[region]]) + + # Format data source + if (data_source == "who") { + data_list <- list(list(ID = 0, + Name = "WHO_NREVSS")) + } else if (data_source == "ilinet") { + data_list <- list(list(ID = 1, + Name = "ILINet")) + } else data_list <- list(list(ID = 0, + Name = "WHO_NREVSS"), + list(ID = 1, + Name = "ILINet")) + + # Format years + year_list <- lapply(seq_along(years), + function(x) list(ID = years[x], + Name = paste(years[x]))) + + # Format sub regions + sub_reg_list <- lapply(seq_along(sub_region_inpt), + function(x) list(ID = sub_region_inpt[x], + Name = paste(sub_region_inpt[x]))) + + params <- list(AppVersion = "Public", + DatasourceDT = data_list, + RegionTypeId = reg, + SeasonsDT = year_list, + SubRegionsDT = sub_reg_list) out_file <- tempfile(fileext=".zip") # CDC API returns a ZIP file so we grab, save & expand it to then read in CSVs - tmp <- httr::POST("https://gis.cdc.gov/grasp/fluview/FluViewPhase2CustomDownload.ashx", + tmp <- httr::POST("https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload", body = params, - write_disk(out_file)) + encode = "json", + httr::write_disk(out_file)) - stop_for_status(tmp) + httr::stop_for_status(tmp) if (!(file.exists(out_file))) stop("Error: cannot process downloaded data") @@ -97,7 +144,17 @@ get_flu_data <- function(region="hhs", sub_region=1:10, suppressMessages(readr::read_csv(x, skip=ct)) }) -> file_list - names(file_list) <- substr(basename(files), 1, 3) + names(file_list) <- substr(basename(files), 1, nchar(basename(files)) - 4) + + # If data are missing, X causes numeric columns to be read as character + purrr::map(file_list, function(x) { + # Create list of columns that should be numeric - exclude character columns + cols <- which(!colnames(x) %in% c("REGION", "REGION TYPE", + "SEASON_DESCRIPTION")) + suppressWarnings(x[cols] <- purrr::map(x[cols], as.numeric)) + return(x) + }) -> file_list + # Depending on the parameters, there could be more than one # file returned. When there's only one, return a more usable @@ -128,3 +185,4 @@ get_flu_data <- function(region="hhs", sub_region=1:10, } } + diff --git a/man/get_flu_data.Rd b/man/get_flu_data.Rd index 7d222cc..a5c3b48 100644 --- a/man/get_flu_data.Rd +++ b/man/get_flu_data.Rd @@ -8,12 +8,15 @@ get_flu_data(region = "hhs", sub_region = 1:10, data_source = "ilinet", years = as.numeric(format(Sys.Date(), "\%Y"))) } \arguments{ -\item{region}{one of "\code{hhs}", "\code{census}", "\code{national}"} +\item{region}{one of "\code{hhs}", "\code{census}", "\code{national}", +"\code{state}"} \item{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}} +For "\code{census}", should be a vector between \code{1:9}.\cr +For "\code{state}", should be a vector of state/territory names +or "\code{all}".} \item{data_source}{either of "\code{who}" (for WHO NREVSS) or "\code{ilinet}" or "\code{all}" (for both)} @@ -49,4 +52,3 @@ There is often a noticeable delay when making the API request to the CDC. flu <- get_flu_data("hhs", 1:10, c("who", "ilinet"), years=2000:2014) } } -