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hrbrmstr 6adf2f86ca Updated httr version requirement 9 years ago
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README.md Updated httr version requirement 9 years ago
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README.md

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).


The CDC's FluView is a Flash portal and the only way to get flu season data is to use GUI controls, making it tedious to retrieve updates. This package uses the same API the portal does to programmatically retrieve data.

The following functions are implemented:

  • get_flu_data : retrieve flu data (national, by various region/sub-region types)
  • get_state_data : retrieve state-level flu data

The following data sets are included:

News

  • Version 0.1 released
  • Version 0.2 released : added state-level data retrieval
  • Version 0.2.1 released : bumped up httr version # requirement in DESCRIPTION

Installation

devtools::install_github("hrbrmstr/cdcfluview")

Usage

suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))

# current verison
packageVersion("cdcfluview")
## [1] '0.2.1'
flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
glimpse(flu)
## Observations: 140
## 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, 2239, 1689, 1173, 1083, 1843, 217, 348, 1201, 61, 386, 2108, 1735, 1501, 1117, 2163,...
## $ TOTAL.PATIENTS    (int) 50896, 134096, 128589, 127408, 106896, 103717, 50032, 36991, 85312, 10868, 50711, 129275,...
## $ NUM..OF.PROVIDERS (int) 142, 253, 242, 299, 266, 236, 83, 117, 227, 53, 148, 242, 238, 305, 277, 246, 83, 114, 24...
## $ X..WEIGHTED.ILI   (dbl) 0.8825503, 1.8170454, 1.2055377, 0.8357537, 0.7384711, 1.8292926, 0.6895413, 0.6733888, 1...
## $ X.UNWEIGHTED.ILI  (dbl) 0.6916064, 1.6696993, 1.3134872, 0.9206643, 1.0131343, 1.7769507, 0.4337224, 0.9407694, 1...
## $ AGE.0.4           (int) 101, 872, 395, 330, 358, 465, 50, 82, 261, 22, 109, 837, 404, 353, 339, 560, 57, 58, 281,...
## $ AGE.5.24          (int) 185, 758, 627, 530, 400, 710, 97, 152, 532, 30, 199, 675, 664, 763, 443, 807, 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, 351, 451, 187, 181, 469, 42, 87, 202, 7, 37, 338, 461, 248, 182, 509, 54, 87, 216, 20...
## $ AGE.50.64         (int) 13, 150, 126, 80, 80, 121, 15, 19, 101, 1, 24, 148, 131, 73, 105, 187, 17, 23, 117, 10, 2...
## $ AGE.65            (int) 9, 108, 90, 46, 64, 78, 13, 8, 105, 1, 17, 110, 75, 64, 48, 100, 11, 12, 97, 3, 8, 108, 8...
state_flu <- get_state_data()
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))
gg <- gg + geom_line()
gg <- gg + facet_wrap(~REGION, ncol=2)
gg <- gg + theme_bw()

gg_s <- state_flu %>%
  filter(WEEKEND=="Jan-03-2015") %>%
  select(state=STATENAME, value=ACTIVITY.LEVEL) %>%
  filter(!(state %in% c("Puerto Rico", "New York City"))) %>% # need to add PR to statebins
  mutate(value=as.numeric(gsub("Level ", "", value))) %>%
  statebins(brewer_pal="RdPu", breaks=4, 
            labels=c("Minimal", "Low", "Moderate", "High"),
            legend_position="bottom", legend_title="ILI Activity Level") +
  ggtitle("CDC State FluView (2015-01-03)")

Test Results

library(cdcfluview)
library(testthat)

date()
## [1] "Mon Jan 12 14:22:33 2015"
test_dir("tests/")
## basic functionality :