### cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal
**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).
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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 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 (high-level) state/territory-level influenza statistics from the CDC
- `get_weekly_flu_report` : Retrieves weekly influenza surveillance report from the CDC
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
- 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
devtools::install_github("hrbrmstr/cdcfluview")
```
### Usage
``` r
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(statebins))
# current verison
packageVersion("cdcfluview")
#> [1] '0.4.0.9000'
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, ...
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))
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-7-1.png" title = "" alt = "" width = "576" / >
``` 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)")
```
< img src = "README_files/README-unnamed-chunk-9-1.png" title = "" alt = "" width = "672" / >
### Test Results
``` r
suppressPackageStartupMessages(library(cdcfluview))
suppressPackageStartupMessages(library(testthat))
date()
#> [1] "Sun Aug 9 09:40:34 2015"
test_dir("tests/")
#> testthat results ========================================================================================================
#> OK: 0 SKIPPED: 0 FAILED: 0
#>
#> DONE
```
