#' Mortality Surveillance Data from the National Center for Health Statistics (deprecated) #' #' 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() { message( paste0( c("This function has been deprecated and will be removed in future releases.", "Use pi_mortality() instead."), collapse="\n" ) ) # 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(readr::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 }