7 changed files with 10 additions and 164 deletions
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#' Mortality Surveillance Data from the National Center for Health Statistics (deprecated) |
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#' |
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#' The National Center for Health Statistics (NCHS) collects and disseminates the Nation's |
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#' official vital statistics. These statistics are based on data provided to NCHS through |
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#' contracts with the vital registration systems operated in the various jurisdictions |
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#' legally responsible for the registration of deaths (i.e., death certificates) and other |
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#' vital events. These data have previously only been released as annual final data files |
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#' 12 months or more after the end of the data year. Recent NCHS efforts to improve the |
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#' timeliness of jurisdiction reporting and modernize the national vital statistics |
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#' infrastructure have created a system capable of supporting near real-time surveillance. |
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#' Capitalizing on these new capabilities, NCHS and CDC’s Influenza Division have |
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#' partnered to pilot the use of NCHS mortality surveillance data for Pneumonia and |
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#' Influenza (P&I) mortality surveillance. |
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#' |
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#' NCHS mortality surveillance data are presented by the week the death occurred. |
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#' Nationally P&I percentages are released two weeks after the week of death to allow for |
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#' collection of enough data to produce a stable P&I percentage at the national level. |
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#' Collection of complete data is not expected, and reliable P&I ratios are not expected |
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#' at the region and state level within this two week period. State and Region level |
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#' counts will be released only after 20% of the expected number of deaths are reported |
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#' through the system. |
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#' |
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#' @references \url{https://www.cdc.gov/flu/weekly/nchs.htm} |
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#' @return a list of \code{tbl_df}s |
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#' @export |
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#' @examples \dontrun{ |
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#' get_mortality_surveillance_data() |
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#' } |
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get_mortality_surveillance_data <- function() { |
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|
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message( |
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paste0( |
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c("This function has been deprecated and will be removed in future releases.", |
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"Use pi_mortality() instead."), |
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collapse="\n" |
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) |
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) |
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|
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# scrape (ugh) web page to get data file links for state mortality data |
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|
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pg <- xml2::read_html("https://www.cdc.gov/flu/weekly/nchs.htm") |
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|
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PREFIX <- "https://www.cdc.gov" |
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|
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xml2::xml_find_all(pg, ".//select[@id='State']/option[contains(@value, 'csv') and |
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contains(@value, 'State_')]") %>% |
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xml2::xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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|
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pb <- dplyr::progress_estimated(length(targets)) |
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purrr::map_df(targets, function(x) { |
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pb$tick()$print() |
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suppressMessages(readr::read_csv(URLencode(x), col_types="ciidii")) |
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}) -> influenza_mortality_by_state |
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|
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# scrape (ugh) web page to get data file links for regional mortality data |
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|
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xml2::xml_find_all(pg, ".//select[@id='Regional Data']/ |
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option[contains(@value, 'csv') and |
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not(contains(@value, 'Week_'))]") %>% |
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xml2::xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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|
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pb <- dplyr::progress_estimated(length(targets)) |
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purrr::map_df(targets, function(x) { |
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pb$tick()$print() |
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suppressMessages(read_csv(URLencode(x), col_types="ciidii")) |
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}) -> influenza_mortality_by_region |
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|
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# scrape (ugh) web page to get data file links for weekly mortality data |
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|
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xml2::xml_find_all(pg, ".//select[@id='Regional Data']/ |
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option[contains(@value, 'csv') and |
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contains(@value, 'Week_')]") %>% |
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xml2::xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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|
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pb <- dplyr::progress_estimated(length(targets)) |
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purrr::map_df(targets, function(x) { |
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pb$tick()$print() |
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suppressMessages(read_csv(URLencode(x), col_types="ciidii")) |
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}) -> influenza_mortality_by_week |
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|
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# if return it all |
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|
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list( |
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by_state = influenza_mortality_by_state, |
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by_region = influenza_mortality_by_region, |
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by_week = influenza_mortality_by_week |
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) -> out |
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|
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class(out) <- c("cfv_mortality", class(out)) |
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out |
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|
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} |
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@ -1,41 +0,0 @@ |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/get-mortality-surveillance-data.r |
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\name{get_mortality_surveillance_data} |
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\alias{get_mortality_surveillance_data} |
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\title{Mortality Surveillance Data from the National Center for Health Statistics (deprecated)} |
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\usage{ |
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get_mortality_surveillance_data() |
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} |
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\value{ |
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a list of \code{tbl_df}s |
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} |
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\description{ |
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The National Center for Health Statistics (NCHS) collects and disseminates the Nation's |
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official vital statistics. These statistics are based on data provided to NCHS through |
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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 |
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partnered to pilot the use of NCHS mortality surveillance data for Pneumonia and |
|||
Influenza (P&I) mortality surveillance. |
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} |
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\details{ |
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NCHS mortality surveillance data are presented by the week the death occurred. |
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Nationally P&I percentages are released two weeks after the week of death to allow for |
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collection of enough data to produce a stable P&I percentage at the national level. |
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Collection of complete data is not expected, and reliable P&I ratios are not expected |
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at the region and state level within this two week period. State and Region level |
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counts will be released only after 20% of the expected number of deaths are reported |
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through the system. |
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} |
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\examples{ |
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\dontrun{ |
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get_mortality_surveillance_data() |
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} |
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} |
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\references{ |
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\url{https://www.cdc.gov/flu/weekly/nchs.htm} |
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} |
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