v0.2 released

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: cdcfluview
 Type: Package
 Title: cdcfluview is package that retrieves the data behind the CDC's FluView portal
-Version: 0.1
-Date: 2015-01-10
+Version: 0.2
+Date: 2015-01-11
 Author: Bob Rudis (@hrbrmstr)
 Maintainer: Bob Rudis <bob@rudis.net>
 Description: The CDC's FluView is a Flash portal and the only way to get flu season

NAMESPACE

@@ -1,4 +1,5 @@
 # Generated by roxygen2 (4.1.0): do not edit by hand
 
 export(get_flu_data)
+export(get_state_data)
 import(httr)

R/cdcfluview.R

@@ -85,3 +85,48 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
   }
 
 }
+
+#' Retrieves the state-level data from the CDC's FluView Portal
+#'
+#' Uses the data source from the CDC' State-levelFluView \url{http://gis.cdc.gov/grasp/fluview/main.html}
+#' and provides state flu reporting data as a single data frame
+#'
+#' @param years a vector of years to retrieve data for (i.e. \code{2014} for CDC flu seasn 2014-2015)
+#' @return A \code{data.frame} of state-level data for the specified seasons
+#' @export
+#' @examples \dontrun{
+#' get_state_dat(2014)
+#' get_state_data(c(2013,2014))
+#' }
+get_state_data <- function(years=2014) {
+
+  if (any(years < 1997))
+    stop("Error: years should be > 1997")
+
+  years <- years - 1960
+
+  out_file <- tempfile(fileext=".zip")
+
+  params <- list(EndMMWRID=0,
+                 StartMMWRID=0,
+                 QueryType=1,
+                 DataMode="STATE",
+                 SeasonsList=years)
+
+  tmp <- POST("http://gis.cdc.gov/grasp/fluview/FluViewPhase1CustomDownload.ashx",
+              body=params,
+              write_disk(out_file))
+
+  stop_for_status(tmp)
+
+  if (!(file.exists(out_file)))
+    stop("Error: cannot process downloaded data")
+
+  out_dir <- tempdir()
+
+  files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
+
+  read.csv(files, header=TRUE, stringsAsFactors=FALSE)
+
+}
+

README.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "README"
 author: "Bob Rudis"
-date: January 10, 2015
+date: January 11, 2015
 output:
   md_document:
     variant: markdown_github
@@ -13,13 +13,15 @@ uses the same API the portal does to programmatically retrieve data.
 
 The following functions are implemented:
 
-- `get_flu_data` : retrieve flu data
+- `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
 
@@ -36,12 +38,16 @@ options(width=120)
 ```{r}
 library(cdcfluview)
 library(ggplot2)
+library(dplyr)
+library(statebins)
 
 # current verison
 packageVersion("cdcfluview")
 
 flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
 
+state_flu <- get_state_data()
+
 dplyr::glimpse(flu)
 
 gg <- ggplot(flu, aes(x=WEEK, y=X..WEIGHTED.ILI, group=REGION))
@@ -54,6 +60,22 @@ gg <- gg + theme_bw()
 gg
 ```
 
+```{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 (2014-01-03)")
+```
+
+```{r echo=FALSE, fig.height=5, fig.width=7}
+gg_s
+```
+
 ### Test Results
 
 ```{r}

README.md

@@ -2,13 +2,15 @@ The CDC's FluView is a Flash portal and the only way to get flu season data is t
 
 The following functions are implemented:
 
--   `get_flu_data` : retrieve flu data
+-   `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
 
@@ -26,7 +28,30 @@ library(cdcfluview)
 
 ``` r
 library(ggplot2)
+library(dplyr)
+```
+
+    ## 
+    ## Attaching package: 'dplyr'
+    ## 
+    ## The following object is masked from 'package:stats':
+    ## 
+    ##     filter
+    ## 
+    ## The following objects are masked from 'package:base':
+    ## 
+    ##     intersect, setdiff, setequal, union
+
+``` r
+library(statebins)
+```
+
+    ## Loading required package: grid
+    ## Loading required package: scales
+    ## Loading required package: gridExtra
+    ## Loading required package: RColorBrewer
 
+``` r
 # current verison
 packageVersion("cdcfluview")
 ```
@@ -36,9 +61,12 @@ packageVersion("cdcfluview")
 ``` r
 flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
 
+state_flu <- get_state_data()
+
 dplyr::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...
@@ -65,6 +93,20 @@ 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 (2014-01-03)")
+```
+
+![](README_files/figure-markdown_github/unnamed-chunk-6-1.png)
+
 ### Test Results
 
 ``` r
@@ -74,7 +116,7 @@ library(testthat)
 date()
 ```
 
-    ## [1] "Sat Jan 10 20:25:05 2015"
+    ## [1] "Sun Jan 11 10:53:36 2015"
 
 ``` r
 test_dir("tests/")

man/get_state_data.Rd

@@ -0,0 +1,25 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/cdcfluview.R
+\name{get_state_data}
+\alias{get_state_data}
+\title{Retrieves the state-level data from the CDC's FluView Portal}
+\usage{
+get_state_data(years = 2014)
+}
+\arguments{
+\item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC flu seasn 2014-2015)}
+}
+\value{
+A \code{data.frame} of state-level data for the specified seasons
+}
+\description{
+Uses the data source from the CDC' State-levelFluView \url{http://gis.cdc.gov/grasp/fluview/main.html}
+and provides state flu reporting data as a single data frame
+}
+\examples{
+\dontrun{
+get_state_dat(2014)
+get_state_data(c(2013,2014))
+}
+}
+