From 441eee2e36a507a5d8eab9d62b8d1ac0dfb7dc76 Mon Sep 17 00:00:00 2001 From: boB Rudis Date: Sun, 5 Nov 2017 13:42:06 -0500 Subject: [PATCH] git fixed --- R/cdcfluview-package.R | 1 - R/get_flu_data.r | 188 --------------------------------- R/get_hosp_data.R | 119 --------------------- R/get_state_data.r | 53 ---------- R/get_weekly_flu_report.r | 58 ---------- R/mortalty.r | 89 ---------------- man/cdcfluview.Rd | 18 ++++ man/get_flu_data.Rd | 54 ---------- man/get_hosp_data.Rd | 44 -------- man/get_mortality_surveillance_data.Rd | 41 ------- man/get_state_data.Rd | 40 ------- man/get_weekly_flu_report.Rd | 31 ------ 12 files changed, 18 insertions(+), 718 deletions(-) delete mode 100644 R/get_flu_data.r delete mode 100644 R/get_hosp_data.R delete mode 100644 R/get_state_data.r delete mode 100644 R/get_weekly_flu_report.r delete mode 100644 R/mortalty.r create mode 100644 man/cdcfluview.Rd delete mode 100644 man/get_flu_data.Rd delete mode 100644 man/get_hosp_data.Rd delete mode 100644 man/get_mortality_surveillance_data.Rd delete mode 100644 man/get_state_data.Rd delete mode 100644 man/get_weekly_flu_report.Rd diff --git a/R/cdcfluview-package.R b/R/cdcfluview-package.R index 3e6dd35..b341ad7 100644 --- a/R/cdcfluview-package.R +++ b/R/cdcfluview-package.R @@ -1,4 +1,3 @@ -======= #' Retrieve 'U.S'.' Flu Season Data from the 'CDC' 'FluView' Portal #' #' The U.S. Centers for Disease Control (CDC) maintains a portal diff --git a/R/get_flu_data.r b/R/get_flu_data.r deleted file mode 100644 index 71dbb39..0000000 --- a/R/get_flu_data.r +++ /dev/null @@ -1,188 +0,0 @@ -#' Retrieves state, regional or national influenza statistics from the CDC -#' -#' Uses the data source from the -#' \href{https://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}", -#' "\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}.\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 -#' 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", "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 = 0 - - 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") - - # Match names of states to numbers for API - if (region == "state") { - sub_region <- tolower(sub_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 - - # format the input parameters to fit the CDC API - - years <- years - 1960 - - 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/flu2/PostPhase02DataDownload", - body = params, - encode = "json", - httr::write_disk(out_file)) - - httr::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, 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 - # structure. - - if (length(file_list) == 1) { - - file_list <- file_list[[1]] - - # when no rows, then it's likely the caller specified the - # current year and the flu season has technically not started yet. - # so help them out and move the year back and get current flu - # season data. - - if ((nrow(file_list) == 0) && - (length(years)==1) && - (years == (as.numeric(format(Sys.Date(), "%Y"))-1960))) { - - message("Adjusting [years] to get current season...") - return(get_flu_data(region=region, sub_region=sub_region, - data_source=data_source, years=years+1960-1)) - } else { - return(file_list) - } - - } else { - return(file_list) - } - -} - diff --git a/R/get_hosp_data.R b/R/get_hosp_data.R deleted file mode 100644 index 42e23d5..0000000 --- a/R/get_hosp_data.R +++ /dev/null @@ -1,119 +0,0 @@ -#' Retrieves influenza hospitalization statistics from the CDC -#' -#' Uses the data source from the -#' \href{https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html}{CDC FluView} -#' and provides influenza hospitalization reporting data as a data frame. -#' -#' @param area one of "\code{flusurvnet}", "\code{eip}", "\code{ihsp}", or two -#' digit state abbreviation for an individual site. Exceptions are -#' New York - Albany ("\code{nya}") and New York - Rochester -#' ("\code{nyr}") -#' @param age_group a vector of age groups to pull data for. Possible values are: -#' "\code{overall}", "\code{0-4y}", "\code{5-17y}, "\code{18-49y}, -#' "\code{50-64y}, "\code{65+y}". -#' @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{2009} -#' @return A single \code{data.frame}. -#' @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{ -#' # All of FluSurv-NET, 50-64 years old, 2010/11-2014/15 flu seasons -#' flu <- get_hosp_data("flusurvnet", "50-64y", years=2010:2014) -#' } -get_hosp_data <- function(area="flusurvnet", age_group="overall", - years=as.numeric(format(Sys.Date(), "%Y")) - 1) { - - area <- tolower(area) - age_group <- tolower(age_group) - - if (!(area %in% c("flusurvnet", "eip", "ihsp", "ca", "co", "ct", "ga", "md", - "mn", "nm", "nya", "nyr", "or", "tn", "id", "ia", "mi", - "oh", "ok", "ri", "sd", "ut"))) - stop("Error: area must be one of flusurvnet, eip, ihsp, or a valid state abbreviation") - - if (length(area) != 1) - stop("Error: can only select one area") - - if (!all(age_group %in% c("overall", "0-4y", "5-17y", "18-49y", - "50-64y", "65+y"))) - stop("Error: invalid age group specified") - - if (any(years < 2009)) - stop("Error: years should be >= 2009") - - # Match names of age groups to numbers for API - age_match <- data.frame(age_group = c("overall", "0-4y", "5-17y", - "18-49y", "50-64y", "65+y"), - code = c(6, 1, 2, 3, 4, 5)) - - age_group_num <- age_match$code[age_match$age_group %in% age_group] - - - # format the input parameters to fit the CDC API - - years <- years - 1960 - - area_match <- data.frame(area = c("flusurvnet", "eip", "ca", "co", "ct", - "ga", "md", "mn", "nm", "nya", "nyr", "or", - "tn", "ihsp", "id", "ia", "mi", "oh", "ok", - "ri", "sd", "ut"), - catch = c(22, 22, 1, 2, 3, 4, 7, 9, 11, 13, 14, 17, - 20, 22, 6, 5, 8, 15, 16, 18, 19, 21), - network = c(1, rep(2, 12), rep(3, 9))) - - # Format years - year_list <- lapply(seq_along(years), - function(x) list(ID = years[x])) - - # Format age group - age_list <- lapply(seq_along(age_group_num), - function(x) list(ID = age_group_num[x])) - - params <- list(AppVersion = "Public", - agegroups = age_list, - catchmentid = area_match$catch[area_match$area == area], - networkid = area_match$network[area_match$area == area], - seasons = year_list) - - out_file <- tempfile(fileext=".json") - - # 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/Flu3/PostPhase03DownloadData", - body = params, - encode = "json", - httr::write_disk(out_file, overwrite = T)) - - httr::stop_for_status(tmp) - - if (!(file.exists(out_file))) - stop("Error: cannot process downloaded data") - - file <- jsonlite::fromJSON(out_file)[[1]] - - # pb <- dplyr::progress_estimated(length(file)) - # purrr::map(file, 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, nchar(basename(files)) - 4) - - # Depending on the parameters, there could be more than one - # file returned. When there's only one, return a more usable - # structure. - - # when no rows, then it's likely the caller specified the - # current year and the flu season has technically not started yet. - # so help them out and move the year back and get current flu - # season data. - - - return(file) - -} diff --git a/R/get_state_data.r b/R/get_state_data.r deleted file mode 100644 index 568d8cd..0000000 --- a/R/get_state_data.r +++ /dev/null @@ -1,53 +0,0 @@ -#' Retrieves state/territory-level influenza statistics from the CDC -#' -#' Uses the data source from the CDC' State-levelFluView -#' \url{https://gis.cdc.gov/grasp/fluview/main.html} and provides state flu -#' reporting data as a single data frame.\cr -#' \cr -#' This function provides similar data to \code{\link{get_weekly_flu_report}} but -#' provides more metadata about the reporting sources and has access to more -#' historical infomation. -#' -#' @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{2008} -#' @return A \code{data.frame} of state-level data for the specified seasons -#' (also classed as \code{cdcstatedata}) -#' @export -#' @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. -#' @examples \dontrun{ -#' get_state_data(2014) -#' get_state_data(c(2013, 2014)) -#' get_state_data(2010:2014) -#' httr::with_verbose(get_state_data(2009:2015)) -#' } -get_state_data <- function(years=as.numeric(format(Sys.Date(), "%Y"))) { - - if (any(years < 2008)) - stop("Error: years should be >= 2008") - - years <- c((years - 1960), 1) - years <- paste0(years, collapse=",") - - tmp <- httr::GET(sprintf("https://gis.cdc.gov/grasp/fluView1/Phase1DownloadDataP/%s", years)) - - stop_for_status(tmp) - - # the API doesn't return actual JSON. It returns a JavaScript data structre - # which is why we need the assistance of the super handy V8 pkg. - - res <- httr::content(tmp, as="parsed") - - ctx <- V8::v8() - ctx$eval(V8::JS(sprintf("var dat=%s;", res))) - res <- ctx$get("dat", flatten=FALSE) - out <- suppressMessages(readr::type_convert(res$datadownload)) - - class(out) <- c("cdcstatedata", class(out)) - - out - -} diff --git a/R/get_weekly_flu_report.r b/R/get_weekly_flu_report.r deleted file mode 100644 index 3b7d4e5..0000000 --- a/R/get_weekly_flu_report.r +++ /dev/null @@ -1,58 +0,0 @@ -#' Retrieves (high-level) weekly influenza surveillance report from the CDC -#' -#' The CDC publishes a \href{https://www.cdc.gov/flu/weekly/usmap.htm}{weekly -#' influenza report} detailing high-level flu activity per-state. They also -#' publish a data file (see \code{References}) of historical report readings. -#' This function reads that XML file and produces a long \code{data_frame} -#' with the historical surveillance readings.\cr -#' \cr -#' This function provides similar data to \code{\link{get_state_data}} but without -#' the reporting source metadata and a limit on the historical flu information. -#' -#' @references \url{https://www.cdc.gov/flu/weekly/flureport.xml} -#' @return \code{tbl_df} (also classed with \code{cdcweeklyreport}) with six -#' columns: \code{year}, \code{week_number}, \code{state}, \code{color}, -#' \code{label}, \code{subtitle} -#' @export -#' @examples \dontrun{ -#' get_weekly_flu_report() -#' } -get_weekly_flu_report <- function() { - - # grab the report - doc <- read_xml("https://www.cdc.gov/flu/weekly/flureport.xml") - - # extract the time periods - periods <- xml_attrs(xml_find_all(doc, "timeperiod")) - - # for each period extract the state information and - # shove it all into a data frame - pb <- progress_estimated(length(periods)) - purrr::map_df(periods, function(period) { - - pb$tick()$print() - - tp <- sprintf("//timeperiod[@number='%s' and @year='%s']", - period["number"], period["year"]) - - weeks <- xml_find_first(doc, tp) - kids <- xml_children(weeks) - - abbrev <- xml_text(xml_find_all(kids, "abbrev"), TRUE) - color <- xml_text(xml_find_all(kids, "color"), TRUE) - label <- xml_text(xml_find_all(kids, "label"), TRUE) - - data_frame(year=period["year"], - week_number=period["number"], - state=abbrev, - color=color, - label=label, - subtitle=period["subtitle"]) - - }) -> out - - class(out) <- c("cdcweeklyreport", class(out)) - - out - -} \ No newline at end of file diff --git a/R/mortalty.r b/R/mortalty.r deleted file mode 100644 index 4939e05..0000000 --- a/R/mortalty.r +++ /dev/null @@ -1,89 +0,0 @@ -#' Mortality Surveillance Data from the National Center for Health Statistics -#' -#' The National Center for Health Statistics (NCHS) collects and disseminates the Nation's -#' official vital statistics. These statistics are based on data provided to NCHS through -#' contracts with the vital registration systems operated in the various jurisdictions -#' legally responsible for the registration of deaths (i.e., death certificates) and other -#' vital events. These data have previously only been released as annual final data files -#' 12 months or more after the end of the data year. Recent NCHS efforts to improve the -#' timeliness of jurisdiction reporting and modernize the national vital statistics -#' infrastructure have created a system capable of supporting near real-time surveillance. -#' Capitalizing on these new capabilities, NCHS and CDC’s Influenza Division have -#' partnered to pilot the use of NCHS mortality surveillance data for Pneumonia and -#' Influenza (P&I) mortality surveillance. -#' -#' NCHS mortality surveillance data are presented by the week the death occurred. -#' Nationally P&I percentages are released two weeks after the week of death to allow for -#' collection of enough data to produce a stable P&I percentage at the national level. -#' Collection of complete data is not expected, and reliable P&I ratios are not expected -#' at the region and state level within this two week period. State and Region level -#' counts will be released only after 20% of the expected number of deaths are reported -#' through the system. -#' -#' @references \url{https://www.cdc.gov/flu/weekly/nchs.htm} -#' @return a list of \code{tbl_df}s -#' @export -#' @examples \dontrun{ -#' get_mortality_surveillance_data() -#' } -get_mortality_surveillance_data <- function() { - - # scrape (ugh) web page to get data file links for state mortality data - - pg <- xml2::read_html("https://www.cdc.gov/flu/weekly/nchs.htm") - - PREFIX <- "https://www.cdc.gov" - - xml2::xml_find_all(pg, ".//select[@id='State']/option[contains(@value, 'csv') and - contains(@value, 'State_')]") %>% - xml2::xml_attr("value") %>% - sprintf("%s%s", PREFIX, .) -> targets - - pb <- dplyr::progress_estimated(length(targets)) - purrr::map_df(targets, function(x) { - pb$tick()$print() - suppressMessages(read_csv(URLencode(x), col_types="ciidii")) - }) -> influenza_mortality_by_state - - # scrape (ugh) web page to get data file links for regional mortality data - - xml2::xml_find_all(pg, ".//select[@id='Regional Data']/ - option[contains(@value, 'csv') and - not(contains(@value, 'Week_'))]") %>% - xml2::xml_attr("value") %>% - sprintf("%s%s", PREFIX, .) -> targets - - pb <- dplyr::progress_estimated(length(targets)) - purrr::map_df(targets, function(x) { - pb$tick()$print() - suppressMessages(read_csv(URLencode(x), col_types="ciidii")) - }) -> influenza_mortality_by_region - - # scrape (ugh) web page to get data file links for weekly mortality data - - xml2::xml_find_all(pg, ".//select[@id='Regional Data']/ - option[contains(@value, 'csv') and - contains(@value, 'Week_')]") %>% - xml2::xml_attr("value") %>% - sprintf("%s%s", PREFIX, .) -> targets - - pb <- dplyr::progress_estimated(length(targets)) - purrr::map_df(targets, function(x) { - pb$tick()$print() - suppressMessages(read_csv(URLencode(x), col_types="ciidii")) - }) -> influenza_mortality_by_week - - # if return it all - - list( - by_state = influenza_mortality_by_state, - by_region = influenza_mortality_by_region, - by_week = influenza_mortality_by_week - ) -> out - - class(out) <- c("cfv_mortality", class(out)) - - out - -} - diff --git a/man/cdcfluview.Rd b/man/cdcfluview.Rd new file mode 100644 index 0000000..727c5e3 --- /dev/null +++ b/man/cdcfluview.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/cdcfluview-package.R +\docType{package} +\name{cdcfluview} +\alias{cdcfluview} +\alias{cdcfluview-package} +\title{Retrieve 'U.S'.' Flu Season Data from the 'CDC' 'FluView' Portal} +\description{ +The U.S. Centers for Disease Control (CDC) maintains a portal +\url{http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for +accessing state, regional and national influenza statistics as well as +Mortality Surveillance Data. The Flash interface makes it difficult and +time-consuming to select and retrieve influenza data. This package +provides functions to access the data provided by the portal's underlying API. +} +\author{ +Bob Rudis (bob@rud.is) +} diff --git a/man/get_flu_data.Rd b/man/get_flu_data.Rd deleted file mode 100644 index a5c3b48..0000000 --- a/man/get_flu_data.Rd +++ /dev/null @@ -1,54 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_flu_data.r -\name{get_flu_data} -\alias{get_flu_data} -\title{Retrieves state, regional or national influenza statistics from the CDC} -\usage{ -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}", -"\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}.\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)} - -\item{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}} -} -\value{ -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. -} -\description{ -Uses the data source from the -\href{https://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. -} -\details{ -A lookup table between HHS regions and their member states/territories -is provided in \code{\link{hhs_regions}}. -} -\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. -} -\examples{ -\dontrun{ -flu <- get_flu_data("hhs", 1:10, c("who", "ilinet"), years=2000:2014) -} -} diff --git a/man/get_hosp_data.Rd b/man/get_hosp_data.Rd deleted file mode 100644 index 38f99ec..0000000 --- a/man/get_hosp_data.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_hosp_data.R -\name{get_hosp_data} -\alias{get_hosp_data} -\title{Retrieves influenza hospitalization statistics from the CDC} -\usage{ -get_hosp_data(area = "flusurvnet", age_group = "overall", - years = as.numeric(format(Sys.Date(), "\%Y")) - 1) -} -\arguments{ -\item{area}{one of "\code{flusurvnet}", "\code{eip}", "\code{ihsp}", or two -digit state abbreviation for an individual site. Exceptions are -New York - Albany ("\code{nya}") and New York - Rochester -("\code{nyr}")} - - -\item{age_group}{a vector of age groups to pull data for. Possible values are: -"\code{overall}", "\code{0-4y}", "\code{5-17y}, "\code{18-49y}, -"\code{50-64y}, "\code{65+y}".} - -\item{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{2009}} -} -\value{ -A single \code{data.frame}. -} -\description{ -Uses the data source from the -\href{https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html}{CDC FluView} -and provides influenza hospitalization reporting data as a data frame. -} -\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. -} -\examples{ -\dontrun{ -# All of FluSurv-NET, 50-64 years old, 2010/11-2014/15 flu seasons -flu <- get_hosp_data("flusurvnet", "50-64y", years=2010:2014) -} -} diff --git a/man/get_mortality_surveillance_data.Rd b/man/get_mortality_surveillance_data.Rd deleted file mode 100644 index bc54b6c..0000000 --- a/man/get_mortality_surveillance_data.Rd +++ /dev/null @@ -1,41 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mortalty.r -\name{get_mortality_surveillance_data} -\alias{get_mortality_surveillance_data} -\title{Mortality Surveillance Data from the National Center for Health Statistics} -\usage{ -get_mortality_surveillance_data() -} -\value{ -a list of \code{tbl_df}s -} -\description{ -The National Center for Health Statistics (NCHS) collects and disseminates the Nation's -official vital statistics. These statistics are based on data provided to NCHS through -contracts with the vital registration systems operated in the various jurisdictions -legally responsible for the registration of deaths (i.e., death certificates) and other -vital events. These data have previously only been released as annual final data files -12 months or more after the end of the data year. Recent NCHS efforts to improve the -timeliness of jurisdiction reporting and modernize the national vital statistics -infrastructure have created a system capable of supporting near real-time surveillance. -Capitalizing on these new capabilities, NCHS and CDC’s Influenza Division have -partnered to pilot the use of NCHS mortality surveillance data for Pneumonia and -Influenza (P&I) mortality surveillance. -} -\details{ -NCHS mortality surveillance data are presented by the week the death occurred. -Nationally P&I percentages are released two weeks after the week of death to allow for -collection of enough data to produce a stable P&I percentage at the national level. -Collection of complete data is not expected, and reliable P&I ratios are not expected -at the region and state level within this two week period. State and Region level -counts will be released only after 20% of the expected number of deaths are reported -through the system. -} -\examples{ -\dontrun{ -get_mortality_surveillance_data() -} -} -\references{ -\url{https://www.cdc.gov/flu/weekly/nchs.htm} -} diff --git a/man/get_state_data.Rd b/man/get_state_data.Rd deleted file mode 100644 index 8700a5e..0000000 --- a/man/get_state_data.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_state_data.r -\name{get_state_data} -\alias{get_state_data} -\title{Retrieves state/territory-level influenza statistics from the CDC} -\usage{ -get_state_data(years = as.numeric(format(Sys.Date(), "\%Y"))) -} -\arguments{ -\item{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{2008}} -} -\value{ -A \code{data.frame} of state-level data for the specified seasons - (also classed as \code{cdcstatedata}) -} -\description{ -Uses the data source from the CDC' State-levelFluView -\url{https://gis.cdc.gov/grasp/fluview/main.html} and provides state flu -reporting data as a single data frame.\cr -\cr -This function provides similar data to \code{\link{get_weekly_flu_report}} but -provides more metadata about the reporting sources and has access to more -historical infomation. -} -\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. -} -\examples{ -\dontrun{ -get_state_data(2014) -get_state_data(c(2013, 2014)) -get_state_data(2010:2014) -httr::with_verbose(get_state_data(2009:2015)) -} -} diff --git a/man/get_weekly_flu_report.Rd b/man/get_weekly_flu_report.Rd deleted file mode 100644 index efa44f7..0000000 --- a/man/get_weekly_flu_report.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get_weekly_flu_report.r -\name{get_weekly_flu_report} -\alias{get_weekly_flu_report} -\title{Retrieves (high-level) weekly influenza surveillance report from the CDC} -\usage{ -get_weekly_flu_report() -} -\value{ -\code{tbl_df} (also classed with \code{cdcweeklyreport}) with six - columns: \code{year}, \code{week_number}, \code{state}, \code{color}, - \code{label}, \code{subtitle} -} -\description{ -The CDC publishes a \href{https://www.cdc.gov/flu/weekly/usmap.htm}{weekly -influenza report} detailing high-level flu activity per-state. They also -publish a data file (see \code{References}) of historical report readings. -This function reads that XML file and produces a long \code{data_frame} -with the historical surveillance readings.\cr -\cr -This function provides similar data to \code{\link{get_state_data}} but without -the reporting source metadata and a limit on the historical flu information. -} -\examples{ -\dontrun{ -get_weekly_flu_report() -} -} -\references{ -\url{https://www.cdc.gov/flu/weekly/flureport.xml} -}