v0.3.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: cdcfluview
 Type: Package
 Title: cdcfluview is package that retrieves the data behind the CDC's FluView portal
-Version: 0.2.1
-Date: 2015-01-11
+Version: 0.3
+Date: 2015-08-07
 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
@@ -13,6 +13,8 @@ BugReports: https://github.com/hrbrmstr/cdcfluview/issues
 License: MIT + file LICENSE
 Suggests:
     testthat
+Imports:
+    httr (>= 0.3.0),
+    pbapply
 Depends:
-    R (>= 3.0.0),
-    httr (>= 0.5.0)
+    R (>= 3.0.0)

NAMESPACE

@@ -1,5 +1,6 @@
-# Generated by roxygen2 (4.1.0.9000): do not edit by hand
+# Generated by roxygen2 (4.1.1): do not edit by hand
 
 export(get_flu_data)
 export(get_state_data)
 import(httr)
+import(pbapply)

R/cdcfluview-package.R

@@ -2,5 +2,5 @@
 #' @name cdcfluview
 #' @docType package
 #' @author Bob Rudis (@@hrbrmstr)
-#' @import httr
+#' @import httr pbapply
 NULL

README.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "README"
 author: "Bob Rudis"
-date: January 11, 2015
+date: August 7, 2015
 output:
   md_document:
     variant: markdown_github
@@ -24,9 +24,10 @@ The following data sets are included:
 
 ### News
 
-- Version 0.1 released
-- Version 0.2 released : added state-level data 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
 

README.md

@@ -13,9 +13,10 @@ The following data sets are included:
 
 ### News
 
--   Version 0.1 released
--   Version 0.2 released : added state-level data 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
 
@@ -36,30 +37,30 @@ suppressPackageStartupMessages(library(magrittr))
 packageVersion("cdcfluview")
 ```
 
-    ## [1] '0.2.1'
+    ## [1] '0.3'
 
 ``` r
 flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
 glimpse(flu)
 ```
 
-    ## Observations: 140
+    ## 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, 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...
+    ## $ 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, 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...
+    ## $ 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, ...
 
 ``` r
 state_flu <- get_state_data()
@@ -157,10 +158,13 @@ suppressPackageStartupMessages(library(testthat))
 date()
 ```
 
-    ## [1] "Mon Jan 12 14:39:51 2015"
+    ## [1] "Sat Aug  8 14:09:26 2015"
 
 ``` r
 test_dir("tests/")
 ```
 
-    ## basic functionality :
+    ## testthat results ========================================================================================================
+    ## OK: 0 SKIPPED: 0 FAILED: 0
+    ## 
+    ## DONE

R/cdcfluview.R → REget_flu_data.r

@@ -12,7 +12,7 @@
 #'        For "\code{hhs}", should be a vector between \code{1:10}.\cr
 #'        For "\code{census}", should be a vector between \code{1:9}
 #' @param data_source either of "\code{who}" (for WHO NREVSS) or "\code{ilinet}" or "\code{all}" (for both)
-#' @param years a vector of years to retrieve data for (i.e. \code{2014} for CDC flu seasn 2014-2015)
+#' @param years a vector of years to retrieve data for (i.e. \code{2014} for CDC flu season 2014-2015)
 #' @return If only a single \code{data_source} is specified, then a single \code{data.frame} is
 #'         returned, otherwise a named list with each \code{data.frame} is returned.
 #' @export
@@ -51,10 +51,10 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
   data_source <- gsub("who", "WHO_NREVSS", data_source)
   data_source <- gsub("ilinet", "ILINet", data_source)
 
-  params <- list(SubRegionsList=sub_region,
+  params <- list(SubRegionsList=paste0(sub_region, collapse=","),
                  DataSources=data_source,
                  RegionID=reg,
-                 SeasonsList=years)
+                 SeasonsList=paste0(years, collapse=","))
 
   out_file <- tempfile(fileext=".zip")
 
@@ -71,7 +71,7 @@ get_flu_data <- function(region="hhs", sub_region=1:10,
 
   files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
 
-  file_list <- lapply(files, function(x) {
+  file_list <- pblapply(files, function(x) {
     ct <- ifelse(grepl("who", x, ignore.case=TRUE), 0, 1)
     read.csv(x, header=TRUE, skip=ct, stringsAsFactors=FALSE)
   })
@@ -85,48 +85,3 @@ 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)
-
-}
-

REget_state_data.r

@@ -0,0 +1,44 @@
+
+#' 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 season 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=paste0(years, collapse=","))
+
+  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)
+
+}

man/cdcfluview.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0.9000): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/cdcfluview-package.R
 \docType{package}
 \name{cdcfluview}

man/get_flu_data.Rd

@@ -1,5 +1,5 @@
-% Generated by roxygen2 (4.1.0.9000): do not edit by hand
-% Please edit documentation in R/cdcfluview.R
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/get_flu_data.r
 \name{get_flu_data}
 \alias{get_flu_data}
 \title{Retrieve CDC flu data}
@@ -17,7 +17,7 @@ For "\code{census}", should be a vector between \code{1:9}}
 
 \item{data_source}{either of "\code{who}" (for WHO NREVSS) or "\code{ilinet}" or "\code{all}" (for both)}
 
-\item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC flu seasn 2014-2015)}
+\item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC flu season 2014-2015)}
 }
 \value{
 If only a single \code{data_source} is specified, then a single \code{data.frame} is

man/get_state_data.Rd

@@ -1,5 +1,5 @@
-% Generated by roxygen2 (4.1.0.9000): do not edit by hand
-% Please edit documentation in R/cdcfluview.R
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/get_state_data.r
 \name{get_state_data}
 \alias{get_state_data}
 \title{Retrieves the state-level data from the CDC's FluView Portal}
@@ -7,7 +7,7 @@
 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)}
+\item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC flu season 2014-2015)}
 }
 \value{
 A \code{data.frame} of state-level data for the specified seasons
@@ -19,7 +19,7 @@ and provides state flu reporting data as a single data frame
 \examples{
 \dontrun{
 get_state_dat(2014)
-get_state_data(c(2013,2014))
+get_state_data(c(2013, 2014))
 }
 }