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Fixes #3

pull/4/head
Bob Rudis 4 years ago
parent
commit
9caf99c812
22 changed files with 271 additions and 159 deletions
  1. +13
    -11
      DESCRIPTION
  2. +9
    -2
      NAMESPACE
  3. +8
    -0
      NEWS.md
  4. +8
    -6
      R/cdcfluview-package.R
  5. +14
    -9
      R/get_flu_data.r
  6. +4
    -3
      R/get_state_data.r
  7. +6
    -3
      R/get_weekly_flu_report.r
  8. +78
    -0
      R/mortalty.r
  9. +10
    -0
      R/zzz.r
  10. +19
    -22
      README.Rmd
  11. +45
    -88
      README.md
  12. BIN
      README_files/README-unnamed-chunk-5-1.png
  13. BIN
      README_files/README-unnamed-chunk-7-1.png
  14. BIN
      README_files/README-unnamed-chunk-9-1.png
  15. +3
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      cdcfluview.Rproj
  16. +6
    -6
      man/cdcfluview.Rd
  17. +1
    -1
      man/census_regions.Rd
  18. +1
    -1
      man/get_flu_data.Rd
  19. +42
    -0
      man/get_mortality_surveillance_data.Rd
  20. +2
    -2
      man/get_state_data.Rd
  21. +1
    -1
      man/get_weekly_flu_report.Rd
  22. +1
    -1
      man/hhs_regions.Rd

+ 13
- 11
DESCRIPTION View File

@ -1,16 +1,16 @@
Package: cdcfluview
Type: Package
Title: Retrieve U.S. Flu Season Data from the CDC FluView Portal
Version: 0.4.1.9000
Date: 2015-08-09
Author: Bob Rudis (@hrbrmstr)
Maintainer: Bob Rudis <bob@rudis.net>
Version: 0.5.0
Date: 2016-09-25
Author: Bob Rudis (bob@rud.is)
Maintainer: Bob Rudis <bob@rud.is>
Description: The U.S. Centers for Disease Control (CDC) maintains a portal
<http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
accessing state, regional and national influenza statistics. 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.
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.
URL: http://github.com/hrbrmstr/cdcfluview
BugReports: https://github.com/hrbrmstr/cdcfluview/issues
License: MIT + file LICENSE
@ -19,9 +19,11 @@ Suggests:
testthat
Imports:
httr (>= 0.3.0),
pbapply,
xml2,
dplyr,
utils
utils,
purrr,
readr
Depends:
R (>= 3.0.0)
R (>= 3.2.0)
RoxygenNote: 5.0.1

+ 9
- 2
NAMESPACE View File

@ -1,10 +1,17 @@
# Generated by roxygen2 (4.1.1): do not edit by hand
# Generated by roxygen2: do not edit by hand
export(get_flu_data)
export(get_mortality_surveillance_data)
export(get_state_data)
export(get_weekly_flu_report)
import(dplyr)
import(httr)
import(pbapply)
import(utils)
import(xml2)
importFrom(purrr,discard)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_df)
importFrom(purrr,map_lgl)
importFrom(readr,read_csv)

+ 8
- 0
NEWS.md View File

@ -0,0 +1,8 @@
# cdcfluview 0.5.0
* Fixed issue with WHO data format change
* Added Mortality Surveillance Data retrieval function
* Switched to readr::read_csv() and since it handles column names
better this will break your scripts until you use the new
column names.

+ 8
- 6
R/cdcfluview-package.R View File

@ -2,13 +2,15 @@
#'
#' The U.S. Centers for Disease Control (CDC) maintains a portal
#' \code{http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for
#' accessing state, regional and national influenza statistics. 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 portal's underlying API.
#' 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 portal's underlying API.
#'
#' @name cdcfluview
#' @docType package
#' @author Bob Rudis (@@hrbrmstr)
#' @import httr pbapply xml2 dplyr utils
#' @author Bob Rudis (bob@@rud.is)
#' @import httr xml2 dplyr utils
#' @importFrom purrr map map_df map_chr map_lgl discard keep
#' @importFrom readr read_csv
NULL

+ 14
- 9
R/get_flu_data.r View File

@ -51,8 +51,8 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
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")))
stop("Error: data_source must be either 'who', 'ilinet' or both")
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")
@ -62,6 +62,9 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
years <- years - 1960
reg <- as.numeric(c("hhs"=1, "census"=2, "national"=3)[[region]])
if ("all" %in% data_source) data_source <- c("who", "ilinet")
data_source <- gsub("who", "WHO_NREVSS", data_source)
data_source <- gsub("ilinet", "ILINet", data_source)
@ -72,9 +75,9 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
out_file <- tempfile(fileext=".zip")
tmp <- POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase2CustomDownload.ashx",
body=params,
write_disk(out_file))
tmp <- httr::POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase2CustomDownload.ashx",
body=params,
write_disk(out_file))
stop_for_status(tmp)
@ -85,10 +88,12 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
file_list <- pblapply(files, function(x) {
ct <- ifelse(grepl("who", x, ignore.case=TRUE), 0, 1)
read.csv(x, header=TRUE, skip=ct, stringsAsFactors=FALSE)
})
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, 3)


+ 4
- 3
R/get_state_data.r View File

@ -19,7 +19,7 @@
#' 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_dat(2014)
#' get_state_data(2014)
#' get_state_data(c(2013, 2014))
#' get_state_data(2010:2014)
#' httr::with_verbose(get_state_data(2009:2015))
@ -39,7 +39,7 @@ get_state_data <- function(years=as.numeric(format(Sys.Date(), "%Y"))) {
DataMode="STATE",
SeasonsList=paste0(years, collapse=","))
tmp <- POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase1CustomDownload.ashx",
tmp <- httr::POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase1CustomDownload.ashx",
body=params,
write_disk(out_file))
@ -52,7 +52,8 @@ get_state_data <- function(years=as.numeric(format(Sys.Date(), "%Y"))) {
files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
out <- read.csv(files, header=TRUE, stringsAsFactors=FALSE)
out <- read.csv(files, header=TRUE, stringsAsFactors=FALSE)
# out <- readr::read_csv(files, col_types="cccccic")
class(out) <- c("cdcstatedata", class(out))


+ 6
- 3
R/get_weekly_flu_report.r View File

@ -27,12 +27,15 @@ get_weekly_flu_report <- function() {
# for each period extract the state information and
# shove it all into a data frame
bind_rows(pblapply(periods, function(period) {
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_one(doc, tp)
weeks <- xml_find_first(doc, tp)
kids <- xml_children(weeks)
abbrev <- xml_text(xml_find_all(kids, "abbrev"), TRUE)
@ -46,7 +49,7 @@ get_weekly_flu_report <- function() {
label=label,
subtitle=period["subtitle"])
})) -> out
}) -> out
class(out) <- c("cdcweeklyreport", class(out))


+ 78
- 0
R/mortalty.r View File

@ -0,0 +1,78 @@
#' 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{http://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() {
pg <- read_html("http://www.cdc.gov/flu/weekly/nchs.htm")
PREFIX <- "http://www.cdc.gov"
xml_find_all(pg, ".//select[@id='State']/option[contains(@value, 'csv') and
contains(@value, 'State_')]") %>%
xml_attr("value") %>%
sprintf("%s%s", PREFIX, .) -> targets
pb <- progress_estimated(length(targets))
map_df(targets, function(x) {
pb$tick()$print()
suppressMessages(read_csv(URLencode(x), col_types="ciidii"))
}) -> influenza_mortality_by_state
xml_find_all(pg, ".//select[@id='Regional Data']/
option[contains(@value, 'csv') and
not(contains(@value, 'Week_'))]") %>%
xml_attr("value") %>%
sprintf("%s%s", PREFIX, .) -> targets
pb <- progress_estimated(length(targets))
map_df(targets, function(x) {
pb$tick()$print()
suppressMessages(read_csv(URLencode(x), col_types="ciidii"))
}) -> influenza_mortality_by_region
xml_find_all(pg, ".//select[@id='Regional Data']/
option[contains(@value, 'csv') and
contains(@value, 'Week_')]") %>%
xml_attr("value") %>%
sprintf("%s%s", PREFIX, .) -> targets
pb <- progress_estimated(length(targets))
map_df(targets, function(x) {
pb$tick()$print()
suppressMessages(read_csv(URLencode(x), col_types="ciidii"))
}) -> influenza_mortality_by_week
list(
by_state=influenza_mortality_by_state,
by_region=influenza_mortality_by_region,
by_week=influenza_mortality_by_week
)
}

+ 10
- 0
R/zzz.r View File

@ -0,0 +1,10 @@
.onAttach <- function(...) {
if (!interactive()) return()
packageStartupMessage(paste0("cdcfluview is under *active* development. ",
"There are *breaking changes*. ",
"See https://github.com/hrbrmstr/cdcfluview for info/news."))
}

+ 19
- 22
README.Rmd View File

@ -1,10 +1,5 @@
---
title: "README"
author: "Bob Rudis"
date: August 9, 2015
output:
md_document:
variant: markdown_github
output: rmarkdown::github_document
---
```{r, echo=FALSE}
@ -19,7 +14,7 @@ knitr::opts_chunk$set(
```
### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](http://cran.r-project.org/web/packages/cdcfluview)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview)
**NOTE** If there's a particular data set from http://www.cdc.gov/flu/weekly/fluviewinteractive.htm that you want and that isn't in the package, please file it as an issue and be as specific as you can (screen shot if possible).
@ -32,6 +27,7 @@ The following functions are implemented:
- `get_flu_data`: Retrieves state, regional or national influenza statistics from the CDC
- `get_state_data`: Retrieves state/territory-level influenza statistics from the CDC
- `get_weekly_flu_report`: Retrieves (high-level) weekly influenza surveillance report from the CDC
- `get_mortality_surveillance_data` : (fairly self explanatory but also pretty new to the pkg and uses data from: http://www.cdc.gov/flu/weekly/nchs.htm
The following data sets are included:
@ -40,6 +36,7 @@ The following data sets are included:
### News
- See NEWS
- Version 0.4.0 - [CRAN release](http://cran.r-project.org/web/packages/cdcfluview)
- Version 0.4.0.999 released : another fix for the CDC API (for region parameter); added data files for HHS/Census region lookups; added weekly high-level flu report retrieval
- Version 0.3 released : fix for the CDC API (it changed how year & region params are encoded in the request)
@ -61,11 +58,11 @@ options(width=120)
### Usage
```{r}
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))
```{r message=FALSE}
library(cdcfluview)
library(ggplot2)
library(dplyr)
library(statebins)
# current verison
packageVersion("cdcfluview")
@ -76,7 +73,7 @@ glimpse(flu)
state_flu <- get_state_data(years=2014)
glimpse(state_flu)
gg <- ggplot(flu, aes(x=WEEK, y=X..WEIGHTED.ILI, group=REGION))
gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
gg <- gg + geom_line()
gg <- gg + facet_wrap(~REGION, ncol=2)
gg <- gg + theme_bw()
@ -86,7 +83,7 @@ gg <- gg + theme_bw()
gg
```
```{r warning=FALSE, error=FALSE, message=FALSE}
```{r eval=FALSE, include=FALSE, warning=FALSE, error=FALSE, message=FALSE}
dat <- get_flu_data(region="hhs",
sub_region=1:10,
data_source="ilinet",
@ -113,13 +110,13 @@ curr_week <- tail(dat, 1)$season_week
gg <- ggplot()
gg <- gg + geom_point(data=prev_years,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="#969696", size=1, alpa=0.25)
aes(x=season_week, y=`% WEIGHTED ILI`, group=season),
color="#969696", size=1, alpha=0.25)
gg <- gg + geom_point(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
aes(x=season_week, y=`% WEIGHTED ILI`, group=season),
color="red", size=1.25, alpha=1)
gg <- gg + geom_line(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
aes(x=season_week, y=`% WEIGHTED ILI`, group=season),
size=1.25, color="#d7301f")
gg <- gg + geom_vline(xintercept=curr_week, color="#d7301f", size=0.5, linetype="dashed", alpha=0.5)
gg <- gg + facet_wrap(~REGION, ncol=3)
@ -136,7 +133,7 @@ gg <- gg + theme(axis.text.x=element_blank())
gg
```
```{r}
```{r message=FALSE}
gg_s <- state_flu %>%
filter(WEEKEND=="Jan-03-2015") %>%
select(state=STATENAME, value=ACTIVITY.LEVEL) %>%
@ -154,9 +151,9 @@ gg_s
### Test Results
```{r}
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(testthat))
```{r message=FALSE}
library(cdcfluview)
library(testthat)
date()


+ 45
- 88
README.md View File

@ -1,6 +1,7 @@
### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal
[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](http://cran.r-project.org/web/packages/cdcfluview)
[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview)
**NOTE** If there's a particular data set from <http://www.cdc.gov/flu/weekly/fluviewinteractive.htm> that you want and that isn't in the package, please file it as an issue and be as specific as you can (screen shot if possible).
@ -13,6 +14,7 @@ The following functions are implemented:
- `get_flu_data`: Retrieves state, regional or national influenza statistics from the CDC
- `get_state_data`: Retrieves state/territory-level influenza statistics from the CDC
- `get_weekly_flu_report`: Retrieves (high-level) weekly influenza surveillance report from the CDC
- `get_mortality_surveillance_data` : (fairly self explanatory but also pretty new to the pkg and uses data from: <http://www.cdc.gov/flu/weekly/nchs.htm>
The following data sets are included:
@ -21,6 +23,7 @@ The following data sets are included:
### News
- See NEWS
- Version 0.4.0 - [CRAN release](http://cran.r-project.org/web/packages/cdcfluview)
- Version 0.4.0.999 released : another fix for the CDC API (for region parameter); added data files for HHS/Census region lookups; added weekly high-level flu report retrieval
- Version 0.3 released : fix for the CDC API (it changed how year & region params are encoded in the request)
@ -39,103 +42,57 @@ devtools::install_github("hrbrmstr/cdcfluview")
### Usage
``` r
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))
library(cdcfluview)
library(ggplot2)
library(dplyr)
library(statebins)
# current verison
packageVersion("cdcfluview")
#> [1] '0.4.1.9000'
#> [1] '0.5.0'
flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
glimpse(flu)
#> Observations: 440
#> Variables:
#> $ REGION.TYPE (chr) "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions",...
#> $ REGION (chr) "Region 1", "Region 2", "Region 3", "Region 4", "Region 5", "Region 6", "Region 7", "Regi...
#> $ YEAR (int) 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014,...
#> $ WEEK (int) 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 4...
#> $ ILITOTAL (int) 352, 2254, 1696, 1182, 1083, 1844, 220, 348, 1329, 61, 386, 2129, 1747, 1517, 1117, 2165,...
#> $ TOTAL.PATIENTS (int) 51688, 137157, 129302, 130419, 107261, 103975, 50272, 37014, 88421, 11172, 51169, 132513,...
#> $ NUM..OF.PROVIDERS (int) 147, 285, 245, 305, 267, 241, 84, 117, 237, 55, 151, 274, 241, 310, 277, 250, 84, 114, 24...
#> $ X..WEIGHTED.ILI (dbl) 0.8306102, 1.7759176, 1.1477759, 0.8167958, 0.7370374, 1.8252298, 0.6970221, 0.6731439, 1...
#> $ X.UNWEIGHTED.ILI (dbl) 0.6810091, 1.6433722, 1.3116580, 0.9063097, 1.0096867, 1.7735032, 0.4376194, 0.9401848, 1...
#> $ AGE.0.4 (int) 101, 869, 395, 333, 358, 465, 50, 82, 310, 22, 109, 837, 404, 356, 339, 560, 57, 58, 335,...
#> $ AGE.5.24 (int) 185, 757, 629, 536, 400, 711, 98, 152, 577, 30, 199, 677, 670, 774, 443, 809, 124, 146, 5...
#> $ AGE.25.64 (lgl) NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N...
#> $ AGE.25.49 (int) 44, 363, 455, 187, 181, 469, 43, 87, 220, 7, 37, 349, 466, 249, 182, 509, 56, 87, 225, 20...
#> $ AGE.50.64 (int) 13, 157, 127, 80, 80, 121, 15, 19, 110, 1, 24, 151, 132, 74, 105, 187, 18, 23, 118, 10, 2...
#> $ AGE.65 (int) 9, 108, 90, 46, 64, 78, 14, 8, 112, 1, 17, 115, 75, 64, 48, 100, 14, 12, 103, 3, 9, 110, ...
#> Observations: 530
#> Variables: 15
#> $ REGION TYPE <chr> "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions",...
#> $ REGION <chr> "Region 1", "Region 2", "Region 3", "Region 4", "Region 5", "Region 6", "Region 7", "Regi...
#> $ YEAR <int> 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014,...
#> $ WEEK <int> 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 4...
#> $ % WEIGHTED ILI <dbl> 0.830610, 1.775920, 1.147780, 0.816796, 0.737037, 1.828510, 0.697022, 0.673507, 1.781290,...
#> $ %UNWEIGHTED ILI <dbl> 0.681009, 1.643370, 1.311660, 0.906310, 1.009690, 1.775430, 0.437619, 0.930417, 1.497090,...
#> $ AGE 0-4 <int> 101, 869, 395, 333, 358, 465, 50, 82, 310, 22, 109, 884, 404, 355, 339, 560, 57, 58, 335,...
#> $ AGE 25-49 <int> 44, 363, 455, 187, 181, 469, 43, 87, 220, 7, 37, 385, 466, 247, 182, 504, 56, 87, 225, 20...
#> $ AGE 25-64 <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N...
#> $ AGE 5-24 <int> 185, 757, 629, 536, 400, 711, 98, 155, 577, 30, 199, 704, 670, 772, 443, 809, 124, 148, 5...
#> $ AGE 50-64 <int> 13, 157, 127, 80, 80, 123, 15, 19, 110, 1, 24, 176, 132, 74, 105, 186, 18, 23, 118, 10, 2...
#> $ AGE 65 <int> 9, 108, 90, 46, 64, 78, 14, 8, 112, 1, 17, 127, 75, 64, 48, 100, 14, 12, 103, 3, 9, 114, ...
#> $ ILITOTAL <int> 352, 2254, 1696, 1182, 1083, 1846, 220, 351, 1329, 61, 386, 2276, 1747, 1512, 1117, 2159,...
#> $ NUM. OF PROVIDERS <int> 147, 285, 244, 305, 267, 241, 84, 120, 240, 55, 151, 275, 241, 311, 277, 250, 84, 116, 24...
#> $ TOTAL PATIENTS <int> 51688, 137157, 129302, 130419, 107261, 103975, 50272, 37725, 88772, 11172, 51169, 134995,...
state_flu <- get_state_data(years=2014)
glimpse(state_flu)
#> Observations: 2809
#> Variables:
#> $ STATENAME (chr) "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama"...
#> $ URL (chr) "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza...
#> $ WEBSITE (chr) "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influen...
#> $ ACTIVITY.LEVEL (chr) "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 5", "Level 10...
#> $ ACTIVITY.LEVEL.LABEL (chr) "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Low", "High", "High...
#> $ WEEKEND (chr) "Oct-04-2014", "Oct-11-2014", "Oct-18-2014", "Oct-25-2014", "Nov-01-2014", "Nov-08-201...
#> $ WEEK (int) 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,...
#> $ SEASON (chr) "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15"...
gg <- ggplot(flu, aes(x=WEEK, y=X..WEIGHTED.ILI, group=REGION))
#> Observations: 2,809
#> Variables: 8
#> $ STATENAME <chr> "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama"...
#> $ URL <chr> "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza...
#> $ WEBSITE <chr> "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influen...
#> $ ACTIVITY.LEVEL <chr> "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 5", "Level 10...
#> $ ACTIVITY.LEVEL.LABEL <chr> "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Low", "High", "High...
#> $ WEEKEND <chr> "Oct-04-2014", "Oct-11-2014", "Oct-18-2014", "Oct-25-2014", "Nov-01-2014", "Nov-08-201...
#> $ WEEK <int> 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,...
#> $ SEASON <chr> "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15", "2014-15"...
gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
gg <- gg + geom_line()
gg <- gg + facet_wrap(~REGION, ncol=2)
gg <- gg + theme_bw()
```
<img src="README_files/README-unnamed-chunk-5-1.png" title="" alt="" width="576" />
``` r
dat <- get_flu_data(region="hhs",
sub_region=1:10,
data_source="ilinet",
years=2000:2014)
dat %>%
mutate(REGION=factor(REGION,
levels=unique(REGION),
labels=c("Boston", "New York",
"Philadelphia", "Atlanta",
"Chicago", "Dallas",
"Kansas City", "Denver",
"San Francisco", "Seattle"),
ordered=TRUE)) %>%
mutate(season_week=ifelse(WEEK>=40, WEEK-40, WEEK),
season=ifelse(WEEK<40,
sprintf("%d-%d", YEAR-1, YEAR),
sprintf("%d-%d", YEAR, YEAR+1))) -> dat
prev_years <- dat %>% filter(season != "2014-2015")
curr_year <- dat %>% filter(season == "2014-2015")
curr_week <- tail(dat, 1)$season_week
gg <- ggplot()
gg <- gg + geom_point(data=prev_years,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="#969696", size=1, alpa=0.25)
gg <- gg + geom_point(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
color="red", size=1.25, alpha=1)
gg <- gg + geom_line(data=curr_year,
aes(x=season_week, y=X..WEIGHTED.ILI, group=season),
size=1.25, color="#d7301f")
gg <- gg + geom_vline(xintercept=curr_week, color="#d7301f", size=0.5, linetype="dashed", alpha=0.5)
gg <- gg + facet_wrap(~REGION, ncol=3)
gg <- gg + labs(x=NULL, y="Weighted ILI Index",
title="ILINet - 1999-2015 year weighted flu index history by CDC region\nWeek Ending Jan 3, 2015 (Red == 2014-2015 season)\n")
gg <- gg + theme_bw()
gg <- gg + theme(panel.grid=element_blank())
gg <- gg + theme(strip.background=element_blank())
gg <- gg + theme(axis.ticks.x=element_blank())
gg <- gg + theme(axis.text.x=element_blank())
```
<img src="README_files/README-unnamed-chunk-5-1.png" width="576" />
<img src="README_files/README-unnamed-chunk-7-1.png" title="" alt="" width="576" />
<img src="README_files/README-unnamed-chunk-7-1.png" width="576" />
``` r
gg_s <- state_flu %>%
@ -149,20 +106,20 @@ gg_s <- state_flu %>%
ggtitle("CDC State FluView (2015-01-03)")
```
<img src="README_files/README-unnamed-chunk-9-1.png" title="" alt="" width="672" />
<img src="README_files/README-unnamed-chunk-9-1.png" width="672" />
### Test Results
``` r
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(testthat))
library(cdcfluview)
library(testthat)
date()
#> [1] "Sun Aug 9 13:13:33 2015"
#> [1] "Mon Sep 26 01:39:06 2016"
test_dir("tests/")
#> testthat results ========================================================================================================
#> OK: 0 SKIPPED: 0 FAILED: 0
#>
#> DONE
#> DONE ===================================================================================================================
```

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cdcfluview.Rproj View File

@ -1,8 +1,8 @@
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
RestoreWorkspace: No
SaveWorkspace: No
AlwaysSaveHistory: No
EnableCodeIndexing: Yes
UseSpacesForTab: Yes


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- 6
man/cdcfluview.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/cdcfluview-package.r
\docType{package}
\name{cdcfluview}
@ -8,12 +8,12 @@
\description{
The U.S. Centers for Disease Control (CDC) maintains a portal
\code{http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for
accessing state, regional and national influenza statistics. 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 portal's underlying API.
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 portal's underlying API.
}
\author{
Bob Rudis (@hrbrmstr)
Bob Rudis (bob@rud.is)
}

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- 1
man/census_regions.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/datasets.r
\docType{data}
\name{census_regions}


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- 1
man/get_flu_data.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% 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}


+ 42
- 0
man/get_mortality_surveillance_data.Rd View File

@ -0,0 +1,42 @@
% 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{http://www.cdc.gov/flu/weekly/nchs.htm}
}

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man/get_state_data.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% 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}
@ -32,7 +32,7 @@ There is often a noticeable delay when making the API request to the CDC. This
}
\examples{
\dontrun{
get_state_dat(2014)
get_state_data(2014)
get_state_data(c(2013, 2014))
get_state_data(2010:2014)
httr::with_verbose(get_state_data(2009:2015))


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man/get_weekly_flu_report.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% 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}


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- 1
man/hhs_regions.Rd View File

@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/datasets.r
\docType{data}
\name{hhs_regions}


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