initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^README\.*Rmd$
+^README\.*html$
+^NOTES\.*Rmd$
+^NOTES\.*html$
+^\.codecov\.yml$
+^README_files$
+^doc$

.codecov.yml

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+comment: false

.gitignore

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+.DS_Store
+.Rproj.user
+.Rhistory
+.RData
+.Rproj
+src/*.o
+src/*.so
+src/*.dll

.travis.yml

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+language: r
+
+warnings_are_errors: true
+
+sudo: required
+
+cache: packages
+
+r:
+ - oldrel
+ - release
+ - devel
+
+apt_packages:
+  - libv8-dev
+  - xclip
+
+env:
+ global:
+   - CRAN: http://cran.rstudio.com
+
+after_success:
+  - Rscript -e 'covr::codecov()'
+
+notifications:
+  email:
+    - bob@rud.is
+  irc:
+    channels:
+      - "104.236.112.222#builds"
+    nick: travisci

DESCRIPTION

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+Package: cdcfluview
+Type: Package
+Title: cdcfluview title goes here otherwise CRAN checks fail
+Version: 0.1.0
+Date: 2017-11-04
+Authors@R: c(
+    person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), 
+           comment = c(ORCID = "0000-0001-5670-2640"))
+  )
+Author: Bob Rudis (bob@rud.is)
+Maintainer: Bob Rudis <bob@rud.is>
+Description: A good description goes here otherwise CRAN checks fail.
+URL: https://github.com/hrbrmstr/cdcfluview
+BugReports: https://github.com/hrbrmstr/cdcfluview/issues
+License: MIT + file LICENSE
+Suggests:
+    testthat,
+    covr
+Depends:
+    R (>= 3.2.0)
+Imports:
+    httr,
+    tools,
+    dplyr,
+    jsonlite,
+    stats
+RoxygenNote: 6.0.1

LICENSE

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+YEAR: 2017
+COPYRIGHT HOLDER: Bob Rudis

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(agd_ipt)
+export(hospitalizations)
+export(ilinet)
+export(who_nrevss)
+import(httr)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,left_join)
+importFrom(jsonlite,fromJSON)
+importFrom(stats,setNames)
+importFrom(tools,file_path_sans_ext)

NEWS.md

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+0.1.0 
+* Initial release

R/aaa.R

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+# CDC U.S. region names to ID map
+.region_map <- c(national=3, hhs=1, census=2, state=5)
+
+# CDC hospital surveillance region map
+.hosp_surv_map <- c(flusurv=1, eip=2, ihsp=3)
+
+# Our bot's user-agent string
+.cdcfluview_ua <- "Mozilla/5.0 (compatible; R-cdcvluview Bot/2.0; https://github.com/hrbrmstr/cdcfluview)"

R/agd-ipt.r

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+#' Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
+#'
+#' Retrieves the age group distribution of influenza positive tests that are reported by
+#' public health laboratories by influenza virus type and subtype/lineage. Laboratory data
+#' from multiple seasons and different age groups is provided.
+#'
+#' @references
+#' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
+#' - [AGD IPT Portal](https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html)
+#' @export
+agd_ipt <- function() {
+  httr::GET(
+    url = "https://gis.cdc.gov/grasp/fluView6/GetFlu6AllDataP",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html"
+    ),
+    httr::verbose(),
+    httr::timeout(60)
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  xdat <- httr::content(res, as="parsed")
+  xdat <- jsonlite::fromJSON(xdat, flatten=TRUE)
+
+  sea_names <- c("seasonid", "sea_description", "sea_startweek", "sea_endweek", "sea_enabled",
+                 "sea_label", "sea_showlabtype")
+  age_names <- c("ageid", "age_label", "age_color_hexvalue", "age_enabled")
+  typ_names <- c("virusid", "vir_description", "vir_label", "vir_startmmwrid", "vir_endmmwrid",
+                 "vir_displayorder", "vir_colorname", "vir_color_hexvalue", "vir_labtypeid",
+                 "vir_sortid")
+  vir_names <- c("virusid", "ageid", "count", "mmwrid", "seasonid", "publishyearweekid", "loaddatetime")
+
+  sea_df <- stats::setNames(xdat$Season, sea_names)
+  age_df <- stats::setNames(xdat$Age, age_names)
+  typ_df <- stats::setNames(xdat$VirusType, typ_names)
+  vir_df <- stats::setNames(xdat$VirusData, vir_names)
+
+  vir_df <- dplyr::left_join(vir_df, sea_df, "seasonid")
+  vir_df <- dplyr::left_join(vir_df, age_df, "ageid")
+  vir_df <- dplyr::left_join(vir_df, typ_df, "virusid")
+  class(vir_df) <- c("tbl_df", "tbl", "data.frame")
+
+  vir_df_cols <- c("sea_label", "age_label", "vir_label", "count", "mmwrid", "seasonid",
+                   "publishyearweekid", "sea_description", "sea_startweek", "sea_endweek",
+                   "vir_description",  "vir_startmmwrid", "vir_endmmwrid")
+
+  vir_df[,vir_df_cols]
+
+}

R/cdcfluview-package.R

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+#' ...
+#'
+#' @name cdcfluview
+#' @docType package
+#' @author Bob Rudis (bob@@rud.is)
+#' @import httr
+#' @importFrom tools file_path_sans_ext
+#' @importFrom dplyr left_join bind_rows %>%
+#' @importFrom jsonlite fromJSON
+#' @importFrom stats setNames
+NULL

R/hospital.r

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+#' Laboratory-Confirmed Influenza Hospitalizations
+#'
+#' @param surveillance_area one of "`flusurv`", "`eip`", or "`ihsp`"
+#' @references
+#' - [Hospital Portal](https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html)
+#' @export
+#' @examples
+#' hosp_fs <- hospitalizations("flusurv")
+#' hosp_eip <- hospitalizations("eip")
+#' hosp_ihsp <- hospitalizations("ihsp")
+hospitalizations <- function(surveillance_area=c("flusurv", "eip", "ihsp")) {
+
+  surveillance_area <- match.arg(tolower(surveillance_area), c("flusurv", "eip", "ihsp"))
+
+  network_id <- .hosp_surv_map[surveillance_area]
+
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/GRASP/Flu3/GetPhase03InitApp?appVersion=Public")
+
+  httr::POST(
+    url = "https://gis.cdc.gov/GRASP/Flu3/PostPhase03GetData",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Origin = "https://gis.cdc.gov",
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
+    ),
+    encode = "json",
+    body = list(
+      appversion = "Public",
+      networkid = network_id,
+      cacthmentid = "22"
+      ),
+    httr::verbose()
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  res <- httr::content(res)
+
+  hosp <- list(res = res, meta = meta)
+
+  age_df <- setNames(hosp$meta$ages, c("age_label", "age", "color"))
+  age_df <- age_df[,c("age", "age_label")]
+
+  sea_df <- setNames(
+    hosp$meta$seasons,
+    c("sea_description", "sea_endweek", "sea_label", "seasonid", "sea_startweek", "color", "color_hexvalue"))
+  sea_df <- sea_df[,c("seasonid", "sea_label", "sea_description", "sea_startweek", "sea_endweek")]
+
+  ser_names <- unlist(hosp$res$busdata$datafields, use.names = FALSE)
+
+  mmwr_df <- bind_rows(hosp$res$mmwr)
+  mmwr_df <- mmwr_df[,c("mmwrid", "weekend", "weeknumber", "weekstart", "year",
+                        "yearweek", "seasonid", "weekendlabel", "weekendlabel2")]
+
+  dplyr::bind_rows(lapply(hosp$res$busdata$dataseries, function(.x) {
+    tdf <- dplyr::bind_rows(lapply(.x$data, function(.x) setNames(.x, ser_names)))
+    tdf$age <- .x$age
+    tdf$season <- .x$season
+    tdf
+  })) -> xdf
+
+  dplyr::left_join(xdf, mmwr_df, c("mmwrid", "weeknumber")) %>%
+    dplyr::left_join(age_df, "age") %>%
+    dplyr::left_join(sea_df, "seasonid")
+
+}

R/ilinet.r

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+#' Retrieve ILINet Surveillance Data
+#'
+#' The CDC FluView Portal provides in-season and past seasons' national, regional,
+#' and state-level outpatient illness and viral surveillance data from both
+#' ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
+#' (National Respiratory and Enteric Virus Surveillance System).
+#'
+#' This function retrieves current and historical ILINet surveillance data for
+#' the identified region.
+#'
+#' @md
+#' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
+#' @references
+#' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
+#' - [ILINet Portal](https://wwwn.cdc.gov/ilinet/) (Login required)
+#' - [WHO/NREVSS](https://www.cdc.gov/surveillance/nrevss/index.html)
+#' @export
+#' @examples
+#' national_ili <- ilinet("national")
+#' hhs_ili <- ilinet("hhs")
+#' census_ili <- ilinet("census")
+#' state_ili <- ilinet("state")
+#' \dontrun{
+#' library(purrr)
+#' map_df(
+#'   c("national", "hhs", "census", "state"),
+#'   ~ilinet(.x) %>% readr::type_convert())
+#' }
+ilinet <- function(region=c("national", "hhs", "census", "state")) {
+
+  region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
+
+  list(
+    AppVersion = "Public",
+    DatasourceDT = list(list(ID = 1, Name = "ILINet")),
+    RegionTypeId = .region_map[region]
+  ) -> params
+
+  params$SubRegionsDT <- switch(region,
+    national = { list(list(ID=0, Name="")) },
+    hhs = { lapply(1:10, function(i) list(ID=i, Name=as.character(i))) },
+    census = { lapply(1:9, function(i) list(ID=i, Name=as.character(i))) },
+    state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
+  )
+
+  seasons <- 37:((unclass(as.POSIXlt(Sys.time()))[["year"]] + 1900) - 1960)
+  params$SeasonsDT <- lapply(seasons, function(i) list(ID=i, Name=as.character(i)))
+
+  tf <- tempfile(fileext = ".zip")
+  td <- tempdir()
+
+  on.exit(unlink(tf), TRUE)
+
+  httr::POST(
+    url = "https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Origin = "https://gis.cdc.gov",
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
+    ),
+    encode = "json",
+    body = params,
+    httr::verbose(),
+    httr::write_disk(tf)
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  nm <- unzip(tf, overwrite = TRUE, exdir = td)
+
+  xdf <- read.csv(nm, skip = 1, stringsAsFactors=FALSE)
+  xdf <- .mcga(xdf)
+  class(xdf) <- c("tbl_df", "tbl", "data.frame")
+
+  xdf[xdf=="X"] <- NA
+
+  xdf
+
+}

R/utils.r

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+.mcga <- function(tbl) {
+
+  x <- colnames(tbl)
+  x <- tolower(x)
+  x <- gsub("[[:punct:][:space:]]+", "_", x)
+  x <- gsub("_+", "_", x)
+  x <- gsub("(^_|_$)", "", x)
+  x <- gsub("^x_", "", x)
+  x <- make.unique(x, sep = "_")
+
+  colnames(tbl) <- x
+
+  tbl
+
+}

R/who-nrvess.r

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+#' Retrieve WHO/NREVSS Surveillance Data
+#'
+#' The CDC FluView Portal provides in-season and past seasons' national, regional,
+#' and state-level outpatient illness and viral surveillance data from both
+#' ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
+#' (National Respiratory and Enteric Virus Surveillance System).
+#'
+#' This function retrieves current and historical WHO/NREVSS surveillance data for
+#' the identified region.
+#'
+#' @md
+#' @note HHS, Census and State data retrieval is not as "instantaneous" as their ILINet
+#'       counterparts.\cr\cr
+#'       Also, beginning for the 2015-16 season, reports from public health and clinical
+#'       laboratories are presented separately in the weekly influenza update. This is
+#'       the reason why a list of data frames is returned.
+#' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
+#' @return list of data frames identified by
+#' - `combined_prior_to_2015_16`
+#' - `public_health_labs`
+#' - `clinical_labs`
+#' @references
+#' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
+#' - [ILINet Portal](https://wwwn.cdc.gov/ilinet/) (Login required)
+#' - [WHO/NREVSS](https://www.cdc.gov/surveillance/nrevss/index.html)
+#' @export
+#' @examples
+#' national_who <- who_nrevss("national")
+#' hhs_who <- who_nrevss("hhs")
+#' census_who <- who_nrevss("census")
+#' state_who <- who_nrevss("state")
+who_nrevss <- function(region=c("national", "hhs", "census", "state")) {
+
+  region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
+
+  list(
+    AppVersion = "Public",
+    DatasourceDT = list(list(ID = 1, Name = "WHO_NREVSS")),
+    RegionTypeId = .region_map[region]
+  ) -> params
+
+  params$SubRegionsDT <- switch(
+    region,
+    national = { list(list(ID=0, Name="")) },
+    hhs = { lapply(1:10, function(i) list(ID=i, Name=as.character(i))) },
+    census = { lapply(1:9, function(i) list(ID=i, Name=as.character(i))) },
+    state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
+  )
+
+  seasons <- 37:((unclass(as.POSIXlt(Sys.time()))[["year"]] + 1900) - 1960)
+  params$SeasonsDT <- lapply(seasons, function(i) list(ID=i, Name=as.character(i)))
+
+  tf <- tempfile(fileext = ".zip")
+  td <- tempdir()
+
+  on.exit(unlink(tf), TRUE)
+
+  httr::POST(
+    url = "https://gis.cdc.gov/grasp/flu2/PostPhase02DataDownload",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Origin = "https://gis.cdc.gov",
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
+    ),
+    encode = "json",
+    body = params,
+    httr::verbose(),
+    httr::timeout(60),
+    httr::write_disk(tf)
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  nm <- unzip(tf, overwrite = TRUE, exdir = td)
+
+  lapply(nm, function(x) {
+
+    tdf <- read.csv(x, skip = 1, stringsAsFactors=FALSE)
+    tdf <- .mcga(tdf)
+    class(tdf) <- c("tbl_df", "tbl", "data.frame")
+
+    tdf[tdf=="X"] <- NA
+
+    tdf
+
+  }) -> xdf
+
+  setNames(xdf, sub("who_nrevss_", "", tools::file_path_sans_ext(tolower(basename(nm)))))
+
+}

README.Rmd

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+---
+output: rmarkdown::github_document
+---
+
+# cdcfluview
+
+## Description
+
+## What's Inside The Tin
+
+The following functions are implemented:
+
+## Installation
+
+```{r eval=FALSE}
+devtools::install_github("hrbrmstr/cdcfluview")
+```
+
+```{r message=FALSE, warning=FALSE, error=FALSE, include=FALSE}
+options(width=120)
+```
+
+## Usage
+
+```{r message=FALSE, warning=FALSE, error=FALSE}
+library(cdcfluview)
+
+# current verison
+packageVersion("cdcfluview")
+
+```
+

cdcfluview.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --resave-data
+PackageRoxygenize: rd,collate,namespace

man/agd_ipt.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/agd-ipt.r
+\name{agd_ipt}
+\alias{agd_ipt}
+\title{Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories}
+\usage{
+agd_ipt()
+}
+\description{
+Retrieves the age group distribution of influenza positive tests that are reported by
+public health laboratories by influenza virus type and subtype/lineage. Laboratory data
+from multiple seasons and different age groups is provided.
+}
+\references{
+- [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
+- [AGD IPT Portal](https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html)
+}

man/cdcfluview.Rd

@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cdcfluview-package.R
+\docType{package}
+\name{cdcfluview}
+\alias{cdcfluview}
+\alias{cdcfluview-package}
+\title{...}
+\description{
+...
+}
+\author{
+Bob Rudis (bob@rud.is)
+}

man/hospitalizations.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/hospital.r
+\name{hospitalizations}
+\alias{hospitalizations}
+\title{Laboratory-Confirmed Influenza Hospitalizations}
+\usage{
+hospitalizations(surveillance_area = c("flusurv", "eip", "ihsp"))
+}
+\arguments{
+\item{surveillance_area}{one of "`flusurv`", "`eip`", or "`ihsp`"}
+}
+\description{
+Laboratory-Confirmed Influenza Hospitalizations
+}
+\examples{
+hosp_fs <- hospitalizations("flusurv")
+hosp_eip <- hospitalizations("eip")
+hosp_ihsp <- hospitalizations("ihsp")
+}
+\references{
+- [Hospital Portal](https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html)
+}

man/ilinet.Rd

@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ilinet.r
+\name{ilinet}
+\alias{ilinet}
+\title{Retrieve ILINet Surveillance Data}
+\usage{
+ilinet(region = c("national", "hhs", "census", "state"))
+}
+\arguments{
+\item{region}{one of "\code{national}", "\code{hhs}", "\code{census}", or "\code{state}"}
+}
+\description{
+The CDC FluView Portal provides in-season and past seasons' national, regional,
+and state-level outpatient illness and viral surveillance data from both
+ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
+(National Respiratory and Enteric Virus Surveillance System).
+}
+\details{
+This function retrieves current and historical ILINet surveillance data for
+the identified region.
+}
+\examples{
+national_ili <- ilinet("national")
+hhs_ili <- ilinet("hhs")
+census_ili <- ilinet("census")
+state_ili <- ilinet("state")
+\dontrun{
+library(purrr)
+map_df(
+  c("national", "hhs", "census", "state"),
+  ~ilinet(.x) \%>\% readr::type_convert())
+}
+}
+\references{
+\itemize{
+\item \href{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}{CDC FluView Portal}
+\item \href{https://wwwn.cdc.gov/ilinet/}{ILINet Portal} (Login required)
+\item \href{https://www.cdc.gov/surveillance/nrevss/index.html}{WHO/NREVSS}
+}
+}

man/who_nrevss.Rd

@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/who-nrvess.r
+\name{who_nrevss}
+\alias{who_nrevss}
+\title{Retrieve WHO/NREVSS Surveillance Data}
+\usage{
+who_nrevss(region = c("national", "hhs", "census", "state"))
+}
+\arguments{
+\item{region}{one of "\code{national}", "\code{hhs}", "\code{census}", or "\code{state}"}
+}
+\value{
+list of data frames identified by
+\itemize{
+\item \code{combined_prior_to_2015_16}
+\item \code{public_health_labs}
+\item \code{clinical_labs}
+}
+}
+\description{
+The CDC FluView Portal provides in-season and past seasons' national, regional,
+and state-level outpatient illness and viral surveillance data from both
+ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS
+(National Respiratory and Enteric Virus Surveillance System).
+}
+\details{
+This function retrieves current and historical WHO/NREVSS surveillance data for
+the identified region.
+}
+\note{
+HHS, Census and State data retrieval is not as "instantaneous" as their ILINet
+counterparts.\cr\cr
+Also, beginning for the 2015-16 season, reports from public health and clinical
+laboratories are presented separately in the weekly influenza update. This is
+the reason why a list of data frames is returned.
+}
+\examples{
+national_who <- who_nrevss("national")
+hhs_who <- who_nrevss("hhs")
+census_who <- who_nrevss("census")
+state_who <- who_nrevss("state")
+}
+\references{
+\itemize{
+\item \href{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}{CDC FluView Portal}
+\item \href{https://wwwn.cdc.gov/ilinet/}{ILINet Portal} (Login required)
+\item \href{https://www.cdc.gov/surveillance/nrevss/index.html}{WHO/NREVSS}
+}
+}

tests/test-all.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_check("cdcfluview")

tests/testthat/test-cdcfluview.R

@@ -0,0 +1,6 @@
+context("basic functionality")
+test_that("we can do something", {
+
+  #expect_that(some_function(), is_a("data.frame"))
+
+})