### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal [![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 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 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 portal's 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. 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: The following data sets are included: - `hhs_regions` HHS Region Table (a data frame with 59 rows and 4 variables) - `census_regions` Census Region Table (a data frame with 51 rows and 2 variables) ### 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) - Version 0.2.1 released : bumped up `httr` version \# requirement in `DESCRIPTION` (via Issue [1](https://github.com/hrbrmstr/cdcfluview/issues/1)) - Version 0.2 released : added state-level data retrieval - Version 0.1 released ### Installation ``` r install.packages("cdcfluview") # **OR** devtools::install_github("hrbrmstr/cdcfluview") ``` ### Usage ``` r library(cdcfluview) library(ggplot2) library(dplyr) library(statebins) # current verison packageVersion("cdcfluview") #> [1] '0.5.0' flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014) glimpse(flu) #> Observations: 530 #> Variables: 15 #> $ REGION TYPE "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions",... #> $ REGION "Region 1", "Region 2", "Region 3", "Region 4", "Region 5", "Region 6", "Region 7", "Regi... #> $ YEAR 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2014,... #> $ WEEK 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 0.830610, 1.775920, 1.147780, 0.816796, 0.737037, 1.828510, 0.697022, 0.673507, 1.781290,... #> $ %UNWEIGHTED ILI 0.681009, 1.643370, 1.311660, 0.906310, 1.009690, 1.775430, 0.437619, 0.930417, 1.497090,... #> $ AGE 0-4 101, 869, 395, 333, 358, 465, 50, 82, 310, 22, 109, 884, 404, 355, 339, 560, 57, 58, 335,... #> $ AGE 25-49 44, 363, 455, 187, 181, 469, 43, 87, 220, 7, 37, 385, 466, 247, 182, 504, 56, 87, 225, 20... #> $ AGE 25-64 NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N... #> $ AGE 5-24 185, 757, 629, 536, 400, 711, 98, 155, 577, 30, 199, 704, 670, 772, 443, 809, 124, 148, 5... #> $ AGE 50-64 13, 157, 127, 80, 80, 123, 15, 19, 110, 1, 24, 176, 132, 74, 105, 186, 18, 23, 118, 10, 2... #> $ AGE 65 9, 108, 90, 46, 64, 78, 14, 8, 112, 1, 17, 127, 75, 64, 48, 100, 14, 12, 103, 3, 9, 114, ... #> $ ILITOTAL 352, 2254, 1696, 1182, 1083, 1846, 220, 351, 1329, 61, 386, 2276, 1747, 1512, 1117, 2159,... #> $ NUM. OF PROVIDERS 147, 285, 244, 305, 267, 241, 84, 120, 240, 55, 151, 275, 241, 311, 277, 250, 84, 116, 24... #> $ TOTAL PATIENTS 51688, 137157, 129302, 130419, 107261, 103975, 50272, 37725, 88772, 11172, 51169, 134995,... state_flu <- get_state_data(years=2014) glimpse(state_flu) #> Observations: 2,809 #> Variables: 8 #> $ STATENAME "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama"... #> $ URL "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza... #> $ WEBSITE "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influen... #> $ ACTIVITY.LEVEL "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 1", "Level 5", "Level 10... #> $ ACTIVITY.LEVEL.LABEL "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Minimal", "Low", "High", "High... #> $ WEEKEND "Oct-04-2014", "Oct-11-2014", "Oct-18-2014", "Oct-25-2014", "Nov-01-2014", "Nov-08-201... #> $ WEEK 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 "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() ```

``` r 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 ``` r library(cdcfluview) library(testthat) date() #> [1] "Mon Sep 26 01:39:06 2016" test_dir("tests/") #> testthat results ======================================================================================================== #> OK: 0 SKIPPED: 0 FAILED: 0 #> #> DONE =================================================================================================================== ```