Bob Rudis
8 years ago
22 changed files with 271 additions and 159 deletions
@ -1,10 +1,17 @@ |
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# Generated by roxygen2 (4.1.1): do not edit by hand |
# Generated by roxygen2: do not edit by hand |
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export(get_flu_data) |
export(get_flu_data) |
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export(get_mortality_surveillance_data) |
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export(get_state_data) |
export(get_state_data) |
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export(get_weekly_flu_report) |
export(get_weekly_flu_report) |
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import(dplyr) |
import(dplyr) |
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import(httr) |
import(httr) |
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import(pbapply) |
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import(utils) |
import(utils) |
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import(xml2) |
import(xml2) |
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importFrom(purrr,discard) |
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importFrom(purrr,keep) |
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importFrom(purrr,map) |
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importFrom(purrr,map_chr) |
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importFrom(purrr,map_df) |
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importFrom(purrr,map_lgl) |
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importFrom(readr,read_csv) |
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@ -0,0 +1,8 @@ |
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# cdcfluview 0.5.0 |
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* Fixed issue with WHO data format change |
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* Added Mortality Surveillance Data retrieval function |
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* Switched to readr::read_csv() and since it handles column names |
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better this will break your scripts until you use the new |
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column names. |
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@ -0,0 +1,78 @@ |
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#' Mortality Surveillance Data from the National Center for Health Statistics |
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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{http://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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pg <- read_html("http://www.cdc.gov/flu/weekly/nchs.htm") |
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PREFIX <- "http://www.cdc.gov" |
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xml_find_all(pg, ".//select[@id='State']/option[contains(@value, 'csv') and |
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contains(@value, 'State_')]") %>% |
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xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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pb <- progress_estimated(length(targets)) |
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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_state |
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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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xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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pb <- progress_estimated(length(targets)) |
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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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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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xml_attr("value") %>% |
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sprintf("%s%s", PREFIX, .) -> targets |
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pb <- progress_estimated(length(targets)) |
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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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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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) |
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} |
@ -0,0 +1,10 @@ |
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.onAttach <- function(...) { |
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if (!interactive()) return() |
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packageStartupMessage(paste0("cdcfluview is under *active* development. ", |
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"There are *breaking changes*. ", |
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"See https://github.com/hrbrmstr/cdcfluview for info/news.")) |
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} |
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Before Width: | Height: | Size: 183 KiB After Width: | Height: | Size: 186 KiB |
Before Width: | Height: | Size: 343 KiB After Width: | Height: | Size: 186 KiB |
Before Width: | Height: | Size: 83 KiB After Width: | Height: | Size: 84 KiB |
@ -0,0 +1,42 @@ |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/mortalty.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} |
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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 |
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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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\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{http://www.cdc.gov/flu/weekly/nchs.htm} |
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} |
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