fixing git

.Rbuildignore

@@ -1,6 +1,18 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
+^README\.*Rmd$
+^README\.*html$
+^NOTES\.*Rmd$
+^NOTES\.*html$
+^\.codecov\.yml$
+^README_files$
+^doc$
+^CONDUCT\.md$
+^codecov\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
 ^.*md$
 ^crunch/
 ^crunch/.*

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 .Rproj.user
 .Rhistory
 .RData

.travis.yml

@@ -12,6 +12,7 @@ r:
  - release
  - devel
 
+<<<<<<< HEAD
 notifications:
   email:
     - bob@rud.is
@@ -21,4 +22,8 @@ notifications:
     nick: travisci
 
 after_success:
-  - Rscript -e 'covr::codecov()'
+  - Rscript -e 'covr::codecov()'
+=======
+after_success:
+  - Rscript -e 'covr::codecov()'
+>>>>>>> c0ce51942c79090d1a9ae3fb95f7e2b292d9302e

CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http:contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

@@ -1,33 +1,37 @@
 Package: cdcfluview
 Type: Package
-Title: Retrieve U.S. Flu Season Data from the CDC FluView Portal
-Version: 0.6.0
-Date: 2017-10-20
-Authors@R: c(person("Bob","Rudis", email = "bob@rud.is", role = c("aut", "cre")),
-  person("Craig", "McGowan", email = "mcgowan.cj@gmail.com", role = "ctb"))
 Encoding: UTF-8
+Title: Retrieve 'U.S'.' Flu Season Data from the 'CDC' 'FluView' Portal
+Version: 0.7.0
+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")),
+    person("Craig", "McGowan", email = "mcgowan.cj@gmail.com", role = "ctb")
+  )
+Author: Bob Rudis (bob@rud.is)
+Maintainer: Bob Rudis <bob@rud.is>
 Description: 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 as well as
     Mortality Surveillance Data. The Flash interface makes it difficult and 
     time-consuming to select and retrieve influenza data. This package 
     provides functions to access the data provided by the portal's underlying API.
-URL: http://github.com/hrbrmstr/cdcfluview
+URL: https://github.com/hrbrmstr/cdcfluview
 BugReports: https://github.com/hrbrmstr/cdcfluview/issues
 License: MIT + file LICENSE
 LazyData: true
 Suggests:
     testthat,
     covr
+Depends:
+    R (>= 3.2.0)
 Imports:
-    httr (>= 0.3.0),
-    xml2,
+    httr,
+    tools,
     dplyr,
-    utils,
-    purrr,
-    readr,
     jsonlite,
-    V8
-Depends:
-    R (>= 3.2.0)
+    stats,
+    utils,
+    sf
 RoxygenNote: 6.0.1

NAMESPACE

@@ -1,21 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
-export(get_flu_data)
-export(get_hosp_data)
-export(get_mortality_surveillance_data)
-export(get_state_data)
-export(get_weekly_flu_report)
-import(V8)
-import(dplyr)
+export(agd_ipt)
+export(cdc_coverage_map)
+export(geographic_spread)
+export(hospitalizations)
+export(ili_weekly_activity_indicators)
+export(ilinet)
+export(pi_mortality)
+export(state_data_providers)
+export(surveillance_areas)
+export(who_nrevss)
 import(httr)
-import(utils)
-import(xml2)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
 importFrom(jsonlite,fromJSON)
-importFrom(purrr,discard)
-importFrom(purrr,keep)
-importFrom(purrr,map)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_df)
-importFrom(purrr,map_lgl)
-importFrom(readr,read_csv)
-importFrom(readr,type_convert)
+importFrom(sf,st_read)
+importFrom(stats,setNames)
+importFrom(tools,file_path_sans_ext)
+importFrom(utils,read.csv)
+importFrom(utils,unzip)

NEWS.md

@@ -1,3 +1,8 @@
+# cdcfluview 0.7.0
+
+* The CDC changed most of their API endpoints to support a new HTML interface.
+  There are many breaking changes but also many new data endpoints.
+
 # cdcfluview 0.5.2
 
 * Modified behavior of `get_flu_data()` to actually grab current flu season
@@ -18,3 +23,6 @@
   better this will break your scripts until you use the new
   column names.
 
+# cdcfluview 0.4.0
+
+* First CRAN release

R/aaa.R

@@ -0,0 +1,15 @@
+# CDC U.S. region names to ID map
+.region_map <- c(national=3, hhs=1, census=2, state=5)
+
+# CDC hospital surveillance surveillance area name to internal pkg use map
+.surv_map <- c(`FluSurv-NET`="flusurv", `EIP`="eip", `IHSP`="ihsp")
+.surv_rev_map <- c(flusurv="FluSurv-NET", eip="EIP", ihsp="IHSP")
+
+# CDC P&I mortality GepID mapping
+.geoid_map <- c(national="1", state="2", region="3")
+
+# Our bot's user-agent string
+.cdcfluview_ua <- "Mozilla/5.0 (compatible; R-cdcvluview Bot/2.0; https://github.com/hrbrmstr/cdcfluview)"
+
+# CDC Basemap
+.cdc_basemap <- "https://gis.cdc.gov/grasp/fluview/FluView1References/data/US_States_w_PR_labels.json"

R/aaa.r

@@ -1 +1,15 @@
-utils::globalVariables(".")
+# CDC U.S. region names to ID map
+.region_map <- c(national=3, hhs=1, census=2, state=5)
+
+# CDC hospital surveillance surveillance area name to internal pkg use map
+.surv_map <- c(`FluSurv-NET`="flusurv", `EIP`="eip", `IHSP`="ihsp")
+.surv_rev_map <- c(flusurv="FluSurv-NET", eip="EIP", ihsp="IHSP")
+
+# CDC P&I mortality GepID mapping
+.geoid_map <- c(national="1", state="2", region="3")
+
+# Our bot's user-agent string
+.cdcfluview_ua <- "Mozilla/5.0 (compatible; R-cdcvluview Bot/2.0; https://github.com/hrbrmstr/cdcfluview)"
+
+# CDC Basemap
+.cdc_basemap <- "https://gis.cdc.gov/grasp/fluview/FluView1References/data/US_States_w_PR_labels.json"

R/agd-ipt.r

@@ -0,0 +1,55 @@
+#' 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
+#' @examples  \dontrun{
+#' agd_ipt()
+#' }
+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

@@ -1,17 +1,22 @@
-#' Retrieve Flu Season Data from the CDC FluView Portal
+=======
+#' Retrieve 'U.S'.' Flu Season Data from the 'CDC' 'FluView' Portal
 #'
 #' The U.S. Centers for Disease Control (CDC) maintains a portal
-#' \code{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for
+#' <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
 #' accessing state, regional and national influenza statistics as well as
-#' Mortality Surveillance Data. The 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.
+#' Mortality Surveillance Data. The Flash interface makes it difficult and
+#' time-consuming to select and retrieve influenza data. This package
+#' provides functions to access the data provided by the portal's underlying API.
 #'
+#' @md
 #' @name cdcfluview
 #' @docType package
 #' @author Bob Rudis (bob@@rud.is)
-#' @import httr xml2 dplyr utils V8
-#' @importFrom purrr map map_df map_chr map_lgl discard keep
-#' @importFrom readr read_csv type_convert
+#' @import httr
+#' @importFrom tools file_path_sans_ext
+#' @importFrom dplyr left_join bind_rows mutate filter %>%
 #' @importFrom jsonlite fromJSON
+#' @importFrom stats setNames
+#' @importFrom sf st_read
+#' @importFrom utils read.csv unzip
 NULL

R/coverage-map.r

@@ -0,0 +1,28 @@
+#' Retrieve CDC U.S. Coverage Map
+#'
+#' The CDC FluView application uses a composite basemap of coverage areas
+#' within the United States that elides and scales Alaska, Hawaii and
+#' Puerto Rico and provides elided and scaled breakouts for New York City
+#' and the District of Columbia.\cr
+#' \cr
+#' The basemap provides polygon identifiers by:
+#' \cr
+#' - `STATE_FIPS`
+#' - `STATE_ABBR`
+#' - `STATE_NAME`
+#' - `HHS_Region`
+#' - `FIPSTXT`)
+#' \cr
+#' This function retrieves the shapefile, projects to EPSG:5069 and
+#' returns it as an `sf` (simple features) object.
+#'
+#' @md
+#' @export
+#' @examples \dontrun{
+#' plot(cdc_coverage_map())
+#' }
+cdc_coverage_map <- function() {
+  xsf <- sf::st_read(.cdc_basemap, quiet=TRUE, stringsAsFactors=FALSE)
+  sf::st_crs(xsf) <- 4326
+  sf::st_transform(xsf, 5069)
+}

R/datasets.r

@@ -39,4 +39,4 @@ NULL
 #' @usage data(census_regions)
 #' @note Last updated 2015-08-09.
 #' @format A data frame with 51 rows and 2 variables
-NULL
+NULL

R/geographic-spread.R

@@ -0,0 +1,38 @@
+#' State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
+#'
+#' @export
+#' @examples \dontrun{
+#' geographic_spread()
+#' }
+geographic_spread <- function() {
+
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/grasp/Flu8/GetPhase08InitApp?appVersion=Public")
+  meta$seasons$seasonid
+
+  httr::POST(
+    url = "https://gis.cdc.gov/grasp/Flu8/PostPhase08DownloadData",
+    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/FluView8.html"
+    ),
+    encode = "json",
+    body = list(
+      AppVersion = "Public",
+      SeasonIDs = paste0(meta$seasons$seasonid, collapse=",")
+    ),
+    httr::timeout(60),
+    httr::verbose()
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  res <- httr::content(res, as="parsed", flatten=TRUE)
+
+  xdf <- dplyr::bind_rows(res$datadownload)
+  xdf$weekend <- as.Date(xdf$weekend, format="%B-%d-%Y")
+
+  xdf
+
+}

R/hospital.r

@@ -0,0 +1,102 @@
+#' Laboratory-Confirmed Influenza Hospitalizations
+#'
+#' @md
+#' @param surveillance_area one of "`flusurv`", "`eip`", or "`ihsp`"
+#' @param region Using "`all`" mimics selecting "Entire Network" from the
+#'        CDC FluView application drop down. Individual regions for each
+#'        surveillance area can also be selected. Use [surveillance_areas()] to
+#'        see a list of valid sub-regions for each surveillance area.
+#' @references
+#' - [Hospital Portal](https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html)
+#' @export
+#' @examples \dontrun{
+#' hosp_fs <- hospitalizations("flusurv")
+#' hosp_eip <- hospitalizations("eip")
+#' hosp_ihsp <- hospitalizations("ihsp")
+#' }
+hospitalizations <- function(surveillance_area=c("flusurv", "eip", "ihsp"),
+                             region="all") {
+
+  sarea <- match.arg(tolower(surveillance_area), choices = c("flusurv", "eip", "ihsp"))
+  sarea <- .surv_rev_map[sarea]
+
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/GRASP/Flu3/GetPhase03InitApp?appVersion=Public")
+  areas <- setNames(meta$catchments[,c("networkid", "name", "area", "catchmentid")],
+                    c("networkid", "surveillance_area", "region", "id"))
+
+  reg <- region
+  if (reg == "all") reg <- "Entire Network"
+
+  tgt <- dplyr::filter(areas, (surveillance_area == sarea) & (region == reg))
+
+  if (nrow(tgt) == 0) {
+    stop("Region not found. Use `surveillance_areas()` to see a list of valid inputs.",
+         call.=FALSE)
+  }
+
+  httr::POST(
+    url = "https://gis.cdc.gov/GRASP/Flu3/PostPhase03GetData",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Origin = "https://gis.cdc.gov",
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html"
+    ),
+    encode = "json",
+    body = list(
+      appversion = "Public",
+      networkid = tgt$networkid,
+      cacthmentid = tgt$id
+    ),
+    httr::verbose()
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  res <- httr::content(res)
+
+  hosp <- list(res = res, meta = meta)
+
+  age_df <- setNames(hosp$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") %>%
+    dplyr::mutate(
+      surveillance_area = sarea,
+      region = reg
+    )
+
+}
+
+#' Retrieve a list of valid sub-regions for each surveillance area.
+#'
+#' @md
+#' @export
+#' @examples
+#' surveillance_areas()
+surveillance_areas <- function() {
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/GRASP/Flu3/GetPhase03InitApp?appVersion=Public")
+  xdf <- setNames(meta$catchments[,c("name", "area")], c("surveillance_area", "region"))
+  xdf$surveillance_area <- .surv_map[xdf$surveillance_area]
+  xdf
+}

R/ili-weekly-state.r

@@ -0,0 +1,80 @@
+#' Retrieve weekly state-level ILI indicators per-state for a given season
+#'
+#' @md
+#' @param season_start_year numeric; start year for flu season (e.g. 2017 for 2017-2018 season)
+#' @references
+#' - [ILI Activity Indicator Map Portal](https://gis.cdc.gov/grasp/fluview/main.html)
+#' @note These statistics use the proportion of outpatient visits to healthcare providers
+#' for influenza-like illness to measure the ILI activity level within a state. They do
+#' not, however, measure the extent of geographic spread of flu within a state. Therefore,
+#'  outbreaks occurring in a single city could cause the state to display high activity levels.\cr
+#' \cr
+#' Data collected in ILINet may disproportionately represent certain populations within
+#' a state, and therefore may not accurately depict the full picture of influenza activity
+#' for the whole state.\cr
+#' \cr
+#' All summary statistics are based on either data collected in ILINet, or reports from
+#' state and territorial epidemiologists. Differences in the summary data presented by
+#' CDC and state health departments likely represent differing levels of data completeness
+#' with data presented by the state likely being the more complete.
+#' @export
+#' @examples \dontrun{
+#' ili_weekly_activity_indicators(2016)
+#' }
+ili_weekly_activity_indicators <- function(season_start_year) {
+
+  jsonlite::fromJSON("https://gis.cdc.gov/grasp/fluView1/Phase1IniP") %>%
+    jsonlite::fromJSON() -> meta
+
+  season <- season_start_year - 1960
+
+  res <- httr::GET(sprintf("https://gis.cdc.gov/grasp/fluView1/Phase1SeasonDataP/%s",
+                           season))
+
+  httr::stop_for_status(res)
+
+  res <- httr::content(res, as="parsed")
+  res <- jsonlite::fromJSON(res)
+
+  setNames(
+    meta$ili_intensity[,c("iliActivityid", "ili_activity_label", "legend")],
+    c("iliactivityid", "ili_activity_label", "ili_activity_group")
+  ) -> iliact
+
+  dplyr::left_join(res$busdata, meta$stateinfo, "stateid") %>%
+    dplyr::left_join(res$mmwr, "mmwrid") %>%
+    dplyr::left_join(iliact, "iliactivityid") -> xdf
+
+  xdf <- xdf[,c("statename", "ili_activity_label", "ili_activity_group",
+                "statefips", "stateabbr", "weekend", "weeknumber", "year", "seasonid")]
+
+  xdf$statefips <- trimws(xdf$statefips)
+  xdf$stateabbr <- trimws(xdf$stateabbr)
+  xdf$weekend <- as.Date(xdf$weekend)
+  xdf$ili_activity_label <- factor(xdf$ili_activity_label,
+                                   levels=iliact$ili_activity_label)
+
+  class(xdf) <- c("tbl_df", "tbl", "data.frame")
+
+  xdf
+
+}
+
+#' Retrieve metadat about U.S. State CDC Provider Data
+#'
+#' @md
+#' @export
+#' @examples
+#' state_data_providers()
+state_data_providers <- function() {
+
+  jsonlite::fromJSON("https://gis.cdc.gov/grasp/fluView1/Phase1IniP") %>%
+    jsonlite::fromJSON() -> meta
+
+  state_info <- meta$stateinfo
+  state_info <- state_info[,c("statename", "statehealthdeptname", "url", "statewebsitename", "statefluphonenum")]
+  class(state_info) <- c("tbl_df", "tbl", "data.frame")
+
+  state_info
+
+}

R/ilinet.r

@@ -0,0 +1,80 @@
+#' 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/pi-mortality.r

@@ -0,0 +1,135 @@
+#' Pneumonia and Influenza Mortality Surveillance
+#'
+#' The National Center for Health Statistics (NCHS) collects and disseminates the Nation's
+#' official vital statistics. NCHS collects death certificate data from state vital
+#' statistics offices for virtually all deaths occurring in the United States. Pneumonia
+#' and influenza (P&I) deaths are identified based on ICD-10
+#' multiple cause of death codes.\cr
+#' \cr
+#' NCHS Mortality Surveillance System data are presented by the week the death occurred
+#' at the national, state, and HHS Region levels. Data on the percentage of deaths due
+#' to P&I on a national level are released two weeks after the week of death to allow
+#' for collection of enough data to produce a stable percentage.  States and HHS regions
+#' with less than 20% of the expected total deaths (average number of total deaths
+#' reported by week during 2008-2012) will be marked as insufficient data. Collection
+#' of complete data is not expected at the time of initial report, and a reliable
+#' percentage of deaths due to P&I is not anticipated at the U.S. Department of Health
+#' and Human Services region or state level within this two week period.  The data for
+#' earlier weeks are continually revised and the proportion of deaths due to P&I may
+#' increase or decrease as new and updated death certificate data are received by NCHS.\cr
+#' \cr
+#' The seasonal baseline of P&I deaths is calculated using a periodic regression model
+#' that incorporates a robust regression procedure applied to data from the previous
+#' five years. An increase of 1.645 standard deviations above the seasonal baseline
+#' of P&I deaths is considered the "epidemic threshold," i.e., the point at which
+#' the observed proportion of deaths attributed to pneumonia or influenza was
+#' significantly higher than would be expected at that time of the year in the
+#' absence of substantial influenza-related mortality. Baselines and thresholds are
+#' calculated at the national and regional level and by age group.
+#'
+#' @md
+#' @param coverage_area coverage area for data (national, state or region)
+#' @note Queries for "state" and "region" are not "instantaneous" and can near or over 30s retrieval delays.
+#' @references
+#' - [Pneumonia and Influenza Mortality Surveillance Portal](https://gis.cdc.gov/grasp/fluview/mortality.html)
+#' @export
+#' @examples \dontrun{
+#' ndf <- pi_mortality()
+#' sdf <- pi_mortality("state")
+#' rdf <- pi_mortality("region")
+#' }
+pi_mortality <- function(coverage_area=c("national", "state", "region")) {
+
+  coverage_area <- match.arg(tolower(coverage_area), choices = c("national", "state", "region"))
+
+  us_states <- read.csv("https://gis.cdc.gov/grasp/fluview/Flu7References/Data/USStates.csv",
+                        stringsAsFactors=FALSE)
+  us_states <- setNames(us_states, c("region_name", "subgeoid", "state_abbr"))
+  us_states <- us_states[,c("region_name", "subgeoid")]
+  us_states$subgeoid <- as.character(us_states$subgeoid)
+
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/grasp/flu7/GetPhase07InitApp?appVersion=Public")
+
+  mapcode_df <- setNames(meta$nchs_mapcode[,c("mapcode", "description")], c("map_code", "callout"))
+  mapcode_df$map_code <- as.character(mapcode_df$map_code)
+
+  geo_df <- meta$nchs_geo_dim
+  geo_df$geoid <- as.character(geo_df$geoid)
+
+  age_df <- setNames(meta$nchs_ages, c("ageid", "age_label"))
+  age_df$ageid <- as.character(age_df$ageid)
+
+  mwmr_df <- meta$mmwr
+  mwmr_df$mmwrid <- as.character(mwmr_df$mmwrid)
+  mwmr_df <- setNames(mwmr_df,
+                      c("mmwrid", "weekend", "mwmr_weeknumber", "weekstart",
+                        "year", "yearweek", "mwmr_seasonid", "mwmr_label", "weekendlabel"))
+
+  sum_df <- meta$nchs_summary
+  sum_df$seasonid <- as.character(sum_df$seasonid)
+  sum_df$ageid <- as.character(sum_df$ageid)
+  sum_df$geoid <- as.character(sum_df$geoid)
+
+  httr::POST(
+    url = "https://gis.cdc.gov/grasp/flu7/PostPhase07DownloadData",
+    httr::user_agent(.cdcfluview_ua),
+    httr::add_headers(
+      Origin = "https://gis.cdc.gov",
+      Accept = "application/json, text/plain, */*",
+      Referer = "https://gis.cdc.gov/grasp/fluview/mortality.html"
+    ),
+    encode = "json",
+    body = list(
+      AppVersion = "Public",
+      AreaParameters = list(list(ID=.geoid_map[coverage_area])),
+      SeasonsParameters = lapply(meta$seasons$seasonid, function(.x) { list(ID=as.integer(.x)) }),
+      AgegroupsParameters = list(list(ID="1"))
+    ),
+    httr::timeout(60),
+    httr::verbose()
+  ) -> res
+
+  httr::stop_for_status(res)
+
+  res <- httr::content(res, as="parsed", flatten=TRUE)
+
+  dplyr::bind_rows(res$seasons) %>%
+    dplyr::left_join(mapcode_df, "map_code") %>%
+    dplyr::left_join(geo_df, "geoid") %>%
+    dplyr::left_join(age_df, "ageid") %>%
+    dplyr::left_join(mwmr_df, "mmwrid") -> xdf
+
+  xdf <- dplyr::mutate(xdf, coverage_area = coverage_area)
+
+  if (coverage_area == "state") {
+    xdf <- dplyr::left_join(xdf, us_states, "subgeoid")
+  } else if (coverage_area == "region") {
+    xdf$region_name <- sprintf("Region %s", xdf$subgeoid)
+  } else {
+    xdf$region_name <- NA_character_
+  }
+
+  xdf[,c("seasonid", "baseline", "threshold", "percent_pni",
+         "percent_complete", "number_influenza", "number_pneumonia",
+         "all_deaths", "Total_PnI", "weeknumber", "geo_description",
+         "age_label", "weekend", "weekstart", "year", "yearweek",
+         "coverage_area", "region_name", "callout")] -> xdf
+
+  suppressWarnings(xdf$baseline <- to_num(xdf$baseline))
+  suppressWarnings(xdf$threshold <- to_num(xdf$threshold))
+  suppressWarnings(xdf$percent_pni <- to_num(xdf$percent_pni) / 100)
+  suppressWarnings(xdf$percent_complete <- to_num(xdf$percent_complete) / 100)
+  suppressWarnings(xdf$number_influenza <- to_num(xdf$number_influenza))
+  suppressWarnings(xdf$number_pneumonia <- to_num(xdf$number_pneumonia))
+  suppressWarnings(xdf$all_deaths <- to_num(xdf$all_deaths))
+  suppressWarnings(xdf$Total_PnI <- to_num(xdf$Total_PnI))
+  suppressWarnings(xdf$weekend <- as.Date(xdf$weekend))
+  suppressWarnings(xdf$weekstart <- as.Date(xdf$weekstart))
+
+  xdf <- .mcga(xdf)
+
+  xdf
+
+}
+
+

R/utils.r

@@ -0,0 +1,24 @@
+.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
+
+}
+
+to_num <- function(x) {
+  x <- gsub("%", "", x, fixed=TRUE)
+  x <- gsub(">", "", x, fixed=TRUE)
+  x <- gsub("<", "", x, fixed=TRUE)
+  x <- gsub(",", "", x, fixed=TRUE)
+  x <- gsub(" ", "", x, fixed=TRUE)
+  as.numeric(x)
+}

R/who-nrvess.r

@@ -0,0 +1,92 @@
+#' 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 \dontrun{
+#' 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)))))
+
+}

R/zzz.r

@@ -1,12 +1,11 @@
 # this is only used during active development phases before/after CRAN releases
 
-# .onAttach <- function(...) {
-#
-#   if (!interactive()) return()
-#
-#   packageStartupMessage(paste0("cdcfluview is under *active* development. ",
-#                                "There are *breaking changes*. ",
-#                                "See https://github.com/hrbrmstr/cdcfluview for info/news."))
-#
-# }
-#
+.onAttach <- function(...) {
+
+  if (!interactive()) return()
+
+  packageStartupMessage(paste0("cdcfluview is under *active* development. ",
+                               "There are *MASSIVE* breaking changes*. ",
+                               "See https://github.com/hrbrmstr/cdcfluview for info/news."))
+
+}

README.Rmd

@@ -1,190 +1,71 @@
 ---
+title: ""
+pagetitle: ""
 output: rmarkdown::github_document
 ---
 
-```{r, echo=FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  warning = FALSE,
-  message = FALSE,
-  comment = "#>",
-  fig.path = "README_files/README-",
-  fig.retina = 2
-)
-```
-### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal
-
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview)
 [![Travis-CI Build Status](https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master)](https://travis-ci.org/hrbrmstr/cdcfluview)
 [![Coverage Status](https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg)](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master)
 
-**NOTE** If there's a particular data set from https://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).
+# I M P O R T A N T
+
+The CDC migrated to a new non-Flash portal and back-end APIs changed. This is a complete reimagining of the package and --- as such --- all your code is going to break. Please use GitHub issues to identify previous API functionality you would like ported over. There's a [release candidate for 0.5.2](https://github.com/hrbrmstr/cdcfluview/releases/tag/v0.5.2) which uses the old API but it likely to break in the near future given the changes to the hidden API. You can do what with `devtools::install_github("hrbrmstr/cdcfluview", ref="58c172b")`.
+
+All folks providing feedback, code or suggestions will be added to the DESCRIPTION file. Please include how you would prefer to be cited in any issues you file.
+
+If there's a particular data set from https://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).
+
+# :mask: cdcfluview
 
------
+Retrieve U.S. Flu Season Data from the CDC FluView Portal
 
-The U.S. Centers for Disease Control (CDC) maintains a [portal](https://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 the portal's underlying API.
+## Description
+
+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 as well as Mortality Surveillance Data. The Flash interface makes it difficult and time-consuming to select and retrieve influenza data. This package provides functions to access the data provided by the portal's underlying API.
+
+## What's Inside The Tin
 
 The following functions are implemented:
 
-- `get_flu_data`:	Retrieves state, regional or national influenza statistics from the CDC
-- `get_state_data`:	Retrieves state/territory-level influenza statistics from the CDC
-- `get_weekly_flu_report`:	Retrieves (high-level) weekly influenza surveillance report from the CDC
-- `get_mortality_surveillance_data` : (fairly self explanatory but also pretty new to the pkg and uses data from: https://www.cdc.gov/flu/weekly/nchs.htm
+- `agd_ipt`:	Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
+- `cdcfluview`:	Tools to Work with the 'CDC' 'FluView' 'API'
+- `cdc_coverage_map`:	Retrieve CDC U.S. Coverage Map
+- `geographic_spread`:	State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
+- `hospitalizations`:	Laboratory-Confirmed Influenza Hospitalizations
+- `ilinet`:	Retrieve ILINet Surveillance Data
+- `ili_weekly_activity_indicators`:	Retrieve weekly state-level ILI indicators per-state for a given season
+- `pi_mortality`:	Pneumonia and Influenza Mortality Surveillance
+- `state_data_providers`:	Retrieve metadat about U.S. State CDC Provider Data
+- `surveillance_areas`:	Retrieve a list of valid sub-regions for each surveillance area.
+- `who_nrevss`:	Retrieve WHO/NREVSS Surveillance Data
 
 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
-
-- See NEWS
-- Version 0.4.0 - [CRAN release](http://cran.r-project.org/web/packages/cdcfluview)
-- 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
+## Installation
 
 ```{r eval=FALSE}
-install.packages("cdcfluview")
-# **OR**
 devtools::install_github("hrbrmstr/cdcfluview")
 ```
 
-```{r echo=FALSE, message=FALSE, warning=FALSE, error=FALSE}
+```{r message=FALSE, warning=FALSE, error=FALSE, include=FALSE}
 options(width=120)
 ```
 
-### Usage
+## Usage
 
-```{r state2015, message=FALSE, warning=FALSE, fig.height=10, fig.width=6}
+```{r message=FALSE, warning=FALSE, error=FALSE}
 library(cdcfluview)
-library(ggplot2)
-library(dplyr)
-library(statebins)
 
 # current verison
 packageVersion("cdcfluview")
-
-flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
-glimpse(flu)
-
-state_flu <- get_state_data(years=2015)
-glimpse(state_flu)
-
-gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
-gg <- gg + geom_line()
-gg <- gg + facet_wrap(~REGION, ncol=2)
-gg <- gg + theme_bw()
-gg
-```
-
-```{r mortality, message=FALSE, warning=FALSE, fig.height=6, fig.width=10}
-msd <- get_mortality_surveillance_data()
-
-mutate(msd$by_state, ym=as.Date(sprintf("%04d-%02d-1", Year, Week), "%Y-%U-%u")) %>% 
-  select(state, wk=ym, death_pct=`Percent of Deaths Due to Pneumonia and Influenza`) %>% 
-  mutate(death_pct=death_pct/100) -> df
-
-gg <- ggplot() + geom_smooth(data=df, aes(wk, death_pct, group=state), 
-                             se=FALSE, color="#2b2b2b", size=0.25) 
-
-gb <- ggplot_build(gg)
-
-gb$data[[1]] %>% 
-  arrange(desc(x)) %>% 
-  group_by(group) %>% 
-  slice(1) %>% 
-  ungroup() %>% 
-  arrange(desc(y)) %>% 
-  head(1) -> top
-
-top_state <- sort(unique(msd$by_state$state))[top$group]
-
-gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state),
-                     hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001)
-gg <- gg + scale_x_date(expand=c(0,0))
-gg <- gg + scale_y_continuous(label=scales::percent)
-gg <- gg + labs(x=NULL, y=NULL,
-                title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)")
-gg <- gg + theme_bw(base_family="Arial Narrow")
-gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0)))
-gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0)))
-gg <- gg + theme(axis.ticks=element_blank())
-gg <- gg + theme(plot.title=element_text(face="bold", size=16))
-gg
 ```
 
-```{r region, eval=FALSE, include=FALSE, warning=FALSE, error=FALSE, message=FALSE}
-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=`% WEIGHTED ILI`, group=season),
-                      color="#969696", size=1, alpha=0.25)
-gg <- gg + geom_point(data=curr_year,
-                      aes(x=season_week, y=`% WEIGHTED ILI`, group=season),
-                      color="red", size=1.25, alpha=1)
-gg <- gg + geom_line(data=curr_year, 
-                     aes(x=season_week, y=`% 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())
-```
-
-```{r bins, message=FALSE, fig.height=5, fig.width=7}
-gg_s <- state_flu %>%
-  filter(weekend=="Jan-02-2016") %>%
-  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)")
-gg_s
-```
+### EXAMPLES COMING SOON
 
-### Test Results
-
-```{r message=FALSE}
-library(cdcfluview)
-library(testthat)
-
-date()
-
-test_dir("tests/")
-```
+## Code of Conduct
 
+Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.

README.md

@@ -1,163 +1,101 @@
 
-### :mask: cdcfluview - Retrieve U.S. Flu Season Data from the CDC FluView Portal
-
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview) [![Travis-CI Build Status](https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master)](https://travis-ci.org/hrbrmstr/cdcfluview) [![Coverage Status](https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg)](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master)
-
-**NOTE** If there's a particular data set from <https://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).
-
-------------------------------------------------------------------------
-
-The U.S. Centers for Disease Control (CDC) maintains a [portal](https://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 the portal's underlying API.
+[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/cdcfluview)](https://cran.r-project.org/package=cdcfluview)
+[![Travis-CI Build
+Status](https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master)](https://travis-ci.org/hrbrmstr/cdcfluview)
+[![Coverage
+Status](https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg)](https://codecov.io/github/hrbrmstr/cdcfluview?branch=master)
+
+I M P O R T A N T
+=================
+
+The CDC migrated to a new non-Flash portal and back-end APIs changed.
+This is a complete reimagining of the package and — as such — all your
+code is going to break. Please use GitHub issues to identify previous
+API functionality you would like ported over. There’s a [release
+candidate for
+0.5.2](https://github.com/hrbrmstr/cdcfluview/releases/tag/v0.5.2) which
+uses the old API but it likely to break in the near future given the
+changes to the hidden API. You can do what with
+`devtools::install_github("hrbrmstr/cdcfluview", ref="58c172b")`.
+
+All folks providing feedback, code or suggestions will be added to the
+DESCRIPTION file. Please include how you would prefer to be cited in any
+issues you file.
+
+If there’s a particular data set from
+<https://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).
+
+:mask: cdcfluview
+=================
+
+Retrieve U.S. Flu Season Data from the CDC FluView Portal
+
+Description
+-----------
+
+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 as well as Mortality
+Surveillance Data. The Flash interface makes it difficult and
+time-consuming to select and retrieve influenza data. This package
+provides functions to access the data provided by the portal’s
+underlying API.
+
+What’s Inside The Tin
+---------------------
 
 The following functions are implemented:
 
--   `get_flu_data`: Retrieves state, regional or national influenza statistics from the CDC
--   `get_state_data`: Retrieves state/territory-level influenza statistics from the CDC
--   `get_weekly_flu_report`: Retrieves (high-level) weekly influenza surveillance report from the CDC
--   `get_mortality_surveillance_data` : (fairly self explanatory but also pretty new to the pkg and uses data from: <https://www.cdc.gov/flu/weekly/nchs.htm>
+-   `agd_ipt`: Age Group Distribution of Influenza Positive Tests
+    Reported by Public Health Laboratories
+-   `cdcfluview`: Tools to Work with the ‘CDC’ ‘FluView’ ‘API’
+-   `cdc_coverage_map`: Retrieve CDC U.S. Coverage Map
+-   `geographic_spread`: State and Territorial Epidemiologists Reports
+    of Geographic Spread of Influenza
+-   `hospitalizations`: Laboratory-Confirmed Influenza Hospitalizations
+-   `ilinet`: Retrieve ILINet Surveillance Data
+-   `ili_weekly_activity_indicators`: Retrieve weekly state-level ILI
+    indicators per-state for a given season
+-   `pi_mortality`: Pneumonia and Influenza Mortality Surveillance
+-   `state_data_providers`: Retrieve metadat about U.S. State CDC
+    Provider Data
+-   `surveillance_areas`: Retrieve a list of valid sub-regions for each
+    surveillance area.
+-   `who_nrevss`: Retrieve WHO/NREVSS Surveillance Data
 
 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
+-   `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)
 
--   See NEWS
--   Version 0.4.0 - [CRAN release](http://cran.r-project.org/web/packages/cdcfluview)
--   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
+Installation
+------------
 
 ``` r
-install.packages("cdcfluview")
-# **OR**
 devtools::install_github("hrbrmstr/cdcfluview")
 ```
 
-### Usage
+Usage
+-----
 
 ``` r
 library(cdcfluview)
-library(ggplot2)
-library(dplyr)
-library(statebins)
 
 # current verison
 packageVersion("cdcfluview")
-#> [1] '0.5.2'
-
-flu <- get_flu_data("hhs", sub_region=1:10, "ilinet", years=2014)
-glimpse(flu)
-#> Observations: 530
-#> Variables: 15
-#> $ 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...
-#> $ % WEIGHTED ILI    <dbl> 0.830610, 1.795830, 1.162260, 0.828920, 0.744546, 1.604740, 0.697022, 0.635856, 1.793140,...
-#> $ %UNWEIGHTED ILI   <dbl> 0.681009, 1.649790, 1.321020, 0.911243, 1.013950, 1.647270, 0.437619, 0.813397, 1.501530,...
-#> $ AGE 0-4           <int> 101, 869, 395, 331, 358, 446, 50, 76, 310, 22, 109, 837, 403, 355, 338, 540, 57, 57, 335,...
-#> $ AGE 25-49         <int> 44, 363, 455, 187, 181, 410, 43, 49, 220, 7, 37, 349, 465, 244, 182, 451, 56, 87, 225, 20...
-#> $ AGE 25-64         <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N...
-#> $ AGE 5-24          <int> 185, 757, 627, 530, 400, 636, 98, 154, 577, 30, 199, 676, 669, 772, 443, 741, 124, 148, 5...
-#> $ AGE 50-64         <int> 13, 157, 126, 80, 80, 111, 15, 19, 110, 1, 24, 151, 130, 74, 105, 168, 18, 23, 118, 10, 2...
-#> $ AGE 65            <int> 9, 107, 89, 46, 64, 77, 14, 8, 112, 1, 17, 115, 75, 64, 48, 97, 14, 12, 103, 3, 9, 114, 8...
-#> $ ILITOTAL          <int> 352, 2253, 1692, 1174, 1083, 1680, 220, 306, 1329, 61, 386, 2128, 1742, 1509, 1116, 1997,...
-#> $ NUM. OF PROVIDERS <int> 146, 276, 234, 299, 261, 226, 84, 119, 237, 55, 150, 265, 232, 306, 271, 235, 84, 115, 24...
-#> $ TOTAL PATIENTS    <int> 51688, 136563, 128083, 128835, 106810, 101987, 50272, 37620, 88510, 11172, 51169, 131884,...
-
-state_flu <- get_state_data(years=2015)
-glimpse(state_flu)
-#> Observations: 2,807
-#> Variables: 8
-#> $ statename            <chr> "Virgin Islands", "District of Columbia", "Virgin Islands", "District of Columbia", "V...
-#> $ url                  <chr> "http://doh.vi.gov/", "http://doh.dc.gov/page/influenza-season", "http://doh.vi.gov/",...
-#> $ website              <chr> "Influenza", "Influenza Information", "Influenza", "Influenza Information", "Influenza...
-#> $ activity_level       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
-#> $ activity_level_label <chr> "Insufficient Data", "Insufficient Data", "Insufficient Data", "Insufficient Data", "I...
-#> $ weekend              <chr> "Oct-10-2015", "Oct-17-2015", "Oct-17-2015", "Oct-24-2015", "Oct-24-2015", "Oct-31-201...
-#> $ season               <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16"...
-#> $ weeknumber           <int> 40, 41, 41, 42, 42, 43, 43, 44, 44, 45, 45, 46, 46, 47, 47, 48, 48, 49, 49, 50, 50, 51...
-
-gg <- ggplot(flu, aes(x=WEEK, y=`% WEIGHTED ILI`, group=REGION))
-gg <- gg + geom_line()
-gg <- gg + facet_wrap(~REGION, ncol=2)
-gg <- gg + theme_bw()
-gg
-```
-
-<img src="README_files/README-state2015-1.png" width="576" />
-
-``` r
-msd <- get_mortality_surveillance_data()
-
-mutate(msd$by_state, ym=as.Date(sprintf("%04d-%02d-1", Year, Week), "%Y-%U-%u")) %>% 
-  select(state, wk=ym, death_pct=`Percent of Deaths Due to Pneumonia and Influenza`) %>% 
-  mutate(death_pct=death_pct/100) -> df
-
-gg <- ggplot() + geom_smooth(data=df, aes(wk, death_pct, group=state), 
-                             se=FALSE, color="#2b2b2b", size=0.25) 
-
-gb <- ggplot_build(gg)
-
-gb$data[[1]] %>% 
-  arrange(desc(x)) %>% 
-  group_by(group) %>% 
-  slice(1) %>% 
-  ungroup() %>% 
-  arrange(desc(y)) %>% 
-  head(1) -> top
-
-top_state <- sort(unique(msd$by_state$state))[top$group]
-
-gg <- gg + geom_text(data=top, aes(as.Date(x, origin="1970-01-01"), y, label=top_state),
-                     hjust=1, family="Arial Narrow", size=3, nudge_x=-5, nudge_y=-0.001)
-gg <- gg + scale_x_date(expand=c(0,0))
-gg <- gg + scale_y_continuous(label=scales::percent)
-gg <- gg + labs(x=NULL, y=NULL,
-                title="Percent of In-State Deaths Due to Pneumonia and Pnfluenza (2010-Present)")
-gg <- gg + theme_bw(base_family="Arial Narrow")
-gg <- gg + theme(axis.text.x=element_text(margin=margin(0,0,0,0)))
-gg <- gg + theme(axis.text.y=element_text(margin=margin(0,0,0,0)))
-gg <- gg + theme(axis.ticks=element_blank())
-gg <- gg + theme(plot.title=element_text(face="bold", size=16))
-gg
 ```
 
-<img src="README_files/README-mortality-1.png" width="960" />
+    ## [1] '0.7.0'
 
-``` r
-gg_s <- state_flu %>%
-  filter(weekend=="Jan-02-2016") %>%
-  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)")
-gg_s
-```
+### EXAMPLES COMING SOON
 
-<img src="README_files/README-bins-1.png" width="672" />
+Code of Conduct
+---------------
 
-### Test Results
-
-``` r
-library(cdcfluview)
-library(testthat)
-
-date()
-#> [1] "Tue Mar 14 09:59:29 2017"
-
-test_dir("tests/")
-#> testthat results ========================================================================================================
-#> OK: 2 SKIPPED: 0 FAILED: 0
-#> 
-#> DONE ===================================================================================================================
-```
+Please note that this project is released with a [Contributor Code of
+Conduct](CONDUCT.md). By participating in this project you agree to
+abide by its terms.

cdcfluview.Rproj

@@ -3,7 +3,6 @@ Version: 1.0
 RestoreWorkspace: No
 SaveWorkspace: No
 AlwaysSaveHistory: No
-
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
 NumSpacesForTab: 2
@@ -20,5 +19,4 @@ PackageInstallArgs: --no-multiarch --with-keep.source
 PackageBuildArgs: --resave-data
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace
-
 QuitChildProcessesOnExit: Yes

man/agd_ipt.Rd

@@ -0,0 +1,22 @@
+% 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.
+}
+\examples{
+ \dontrun{
+agd_ipt()
+}
+}
+\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/cdc_coverage_map.Rd

@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/coverage-map.r
+\name{cdc_coverage_map}
+\alias{cdc_coverage_map}
+\title{Retrieve CDC U.S. Coverage Map}
+\usage{
+cdc_coverage_map()
+}
+\description{
+The CDC FluView application uses a composite basemap of coverage areas
+within the United States that elides and scales Alaska, Hawaii and
+Puerto Rico and provides elided and scaled breakouts for New York City
+and the District of Columbia.\cr
+\cr
+The basemap provides polygon identifiers by:
+\cr
+\itemize{
+\item \code{STATE_FIPS}
+\item \code{STATE_ABBR}
+\item \code{STATE_NAME}
+\item \code{HHS_Region}
+\item \code{FIPSTXT})
+\cr
+This function retrieves the shapefile, projects to EPSG:5069 and
+returns it as an \code{sf} (simple features) object.
+}
+}
+\examples{
+\dontrun{
+plot(cdc_coverage_map())
+}
+}

man/cdcfluview.Rd

@@ -1,18 +0,0 @@
-% 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{Retrieve Flu Season Data from the CDC FluView Portal}
-\description{
-The U.S. Centers for Disease Control (CDC) maintains a portal
-\code{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html} for
-accessing state, regional and national influenza statistics as well as
-Mortality Surveillance Data. The 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.
-}
-\author{
-Bob Rudis (bob@rud.is)
-}

man/geographic_spread.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/geographic-spread.R
+\name{geographic_spread}
+\alias{geographic_spread}
+\title{State and Territorial Epidemiologists Reports of Geographic Spread of Influenza}
+\usage{
+geographic_spread()
+}
+\description{
+State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
+}
+\examples{
+\dontrun{
+geographic_spread()
+}
+}

man/hospitalizations.Rd

@@ -0,0 +1,32 @@
+% 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"),
+  region = "all")
+}
+\arguments{
+\item{surveillance_area}{one of "\code{flusurv}", "\code{eip}", or "\code{ihsp}"}
+
+\item{region}{Using "\code{all}" mimics selecting "Entire Network" from the
+CDC FluView application drop down. Individual regions for each
+surveillance area can also be selected. Use \code{\link[=surveillance_areas]{surveillance_areas()}} to
+see a list of valid sub-regions for each surveillance area.}
+}
+\description{
+Laboratory-Confirmed Influenza Hospitalizations
+}
+\examples{
+\dontrun{
+hosp_fs <- hospitalizations("flusurv")
+hosp_eip <- hospitalizations("eip")
+hosp_ihsp <- hospitalizations("ihsp")
+}
+}
+\references{
+\itemize{
+\item \href{https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html}{Hospital Portal}
+}
+}

man/ili_weekly_activity_indicators.Rd

@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ili-weekly-state.r
+\name{ili_weekly_activity_indicators}
+\alias{ili_weekly_activity_indicators}
+\title{Retrieve weekly state-level ILI indicators per-state for a given season}
+\usage{
+ili_weekly_activity_indicators(season_start_year)
+}
+\arguments{
+\item{season_start_year}{numeric; start year for flu season (e.g. 2017 for 2017-2018 season)}
+}
+\description{
+Retrieve weekly state-level ILI indicators per-state for a given season
+}
+\note{
+These statistics use the proportion of outpatient visits to healthcare providers
+for influenza-like illness to measure the ILI activity level within a state. They do
+not, however, measure the extent of geographic spread of flu within a state. Therefore,
+outbreaks occurring in a single city could cause the state to display high activity levels.\cr
+\cr
+Data collected in ILINet may disproportionately represent certain populations within
+a state, and therefore may not accurately depict the full picture of influenza activity
+for the whole state.\cr
+\cr
+All summary statistics are based on either data collected in ILINet, or reports from
+state and territorial epidemiologists. Differences in the summary data presented by
+CDC and state health departments likely represent differing levels of data completeness
+with data presented by the state likely being the more complete.
+}
+\examples{
+\dontrun{
+ili_weekly_activity_indicators(2016)
+}
+}
+\references{
+\itemize{
+\item \href{https://gis.cdc.gov/grasp/fluview/main.html}{ILI Activity Indicator Map Portal}
+}
+}

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/pi_mortality.Rd

@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pi-mortality.r
+\name{pi_mortality}
+\alias{pi_mortality}
+\title{Pneumonia and Influenza Mortality Surveillance}
+\usage{
+pi_mortality(coverage_area = c("national", "state", "region"))
+}
+\arguments{
+\item{coverage_area}{coverage area for data (national, state or region)}
+}
+\description{
+The National Center for Health Statistics (NCHS) collects and disseminates the Nation's
+official vital statistics. NCHS collects death certificate data from state vital
+statistics offices for virtually all deaths occurring in the United States. Pneumonia
+and influenza (P&I) deaths are identified based on ICD-10
+multiple cause of death codes.\cr
+\cr
+NCHS Mortality Surveillance System data are presented by the week the death occurred
+at the national, state, and HHS Region levels. Data on the percentage of deaths due
+to P&I on a national level are released two weeks after the week of death to allow
+for collection of enough data to produce a stable percentage.  States and HHS regions
+with less than 20% of the expected total deaths (average number of total deaths
+reported by week during 2008-2012) will be marked as insufficient data. Collection
+of complete data is not expected at the time of initial report, and a reliable
+percentage of deaths due to P&I is not anticipated at the U.S. Department of Health
+and Human Services region or state level within this two week period.  The data for
+earlier weeks are continually revised and the proportion of deaths due to P&I may
+increase or decrease as new and updated death certificate data are received by NCHS.\cr
+\cr
+The seasonal baseline of P&I deaths is calculated using a periodic regression model
+that incorporates a robust regression procedure applied to data from the previous
+five years. An increase of 1.645 standard deviations above the seasonal baseline
+of P&I deaths is considered the "epidemic threshold," i.e., the point at which
+the observed proportion of deaths attributed to pneumonia or influenza was
+significantly higher than would be expected at that time of the year in the
+absence of substantial influenza-related mortality. Baselines and thresholds are
+calculated at the national and regional level and by age group.
+}
+\note{
+Queries for "state" and "region" are not "instantaneous" and can near or over 30s retrieval delays.
+}
+\examples{
+\dontrun{
+ndf <- pi_mortality()
+sdf <- pi_mortality("state")
+rdf <- pi_mortality("region")
+}
+}
+\references{
+\itemize{
+\item \href{https://gis.cdc.gov/grasp/fluview/mortality.html}{Pneumonia and Influenza Mortality Surveillance Portal}
+}
+}

man/state_data_providers.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ili-weekly-state.r
+\name{state_data_providers}
+\alias{state_data_providers}
+\title{Retrieve metadat about U.S. State CDC Provider Data}
+\usage{
+state_data_providers()
+}
+\description{
+Retrieve metadat about U.S. State CDC Provider Data
+}
+\examples{
+state_data_providers()
+}

man/surveillance_areas.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/hospital.r
+\name{surveillance_areas}
+\alias{surveillance_areas}
+\title{Retrieve a list of valid sub-regions for each surveillance area.}
+\usage{
+surveillance_areas()
+}
+\description{
+Retrieve a list of valid sub-regions for each surveillance area.
+}
+\examples{
+surveillance_areas()
+}

man/who_nrevss.Rd

@@ -0,0 +1,51 @@
+% 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{
+\dontrun{
+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/testthat/test-cdcfluview.R

@@ -1,24 +1,4 @@
 context("basic functionality")
 test_that("we can do something", {
-
-  skip_on_cran()
-
-  expect_that(dim(get_flu_data("hhs", years=2015)), equals(c(520L, 15L)))
-
-  expect_that(dim(get_state_data(2008)), equals(c(2494L, 8L)))
-
-  invisible(get_flu_data())
-
-  invisible(get_flu_data(data_source="all"))
-
-  invisible(get_weekly_flu_report())
-
+  #expect_that(some_function(), is_a("data.frame"))
 })
-
-test_that("these are potentially time-consuming calls", {
-
-  skip_on_cran()
-
-  invisible(get_mortality_surveillance_data())
-
-})