cdcfluview/README.md

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 releases : added state-level data retrieval

### 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] '0.2'

``` r
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...

``` r
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"...

``` r
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()
```

![](README_files/figure-markdown_github/unnamed-chunk-4-1.png)

``` 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)")
```

![](README_files/figure-markdown_github/unnamed-chunk-6-1.png)

### Test Results

``` r
library(cdcfluview)
library(testthat)

date()
```

    ## [1] "Sun Jan 11 11:05:26 2015"

``` r
test_dir("tests/")
```

    ## basic functionality :