--- title: "" pagetitle: "" output: rmarkdown::github_document --- [![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 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: - `agd_ipt`: Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories - `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) ## 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) library(tidyverse) # current verison packageVersion("cdcfluview") ``` ### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories ```{r message=FALSE, warning=FALSE} glimpse(agd_ipt()) ``` ### Retrieve CDC U.S. Coverage Map ```{r message=FALSE, warning=FALSE} plot(cdc_coverage_map()) ``` ### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza ```{r message=FALSE, warning=FALSE} glimpse(geographic_spread()) ``` ### Laboratory-Confirmed Influenza Hospitalizations ```{r message=FALSE, warning=FALSE} surveillance_areas() glimpse(hospitalizations("flusurv")) glimpse(hospitalizations("eip")) glimpse(hospitalizations("eip", "Colorado")) glimpse(hospitalizations("ihsp")) glimpse(hospitalizations("ihsp", "Oklahoma")) ``` ### Retrieve ILINet Surveillance Data ```{r message=FALSE, warning=FALSE} ilinet("national") ilinet("hhs") ilinet("census") ilinet("state") ``` ### Retrieve weekly state-level ILI indicators per-state for a given season ```{r message=FALSE, warning=FALSE} ili_weekly_activity_indicators(2017) ili_weekly_activity_indicators(2015) ``` ### Pneumonia and Influenza Mortality Surveillance ```{r message=FALSE, warning=FALSE} pi_mortality("national") pi_mortality("state") pi_mortality("region") ``` ### Retrieve metadat about U.S. State CDC Provider Data ```{r message=FALSE, warning=FALSE} ``` ### Retrieve a list of valid sub-regions for each surveillance area. ```{r message=FALSE, warning=FALSE} state_data_providers() ``` ### Retrieve WHO/NREVSS Surveillance Data ```{r message=FALSE, warning=FALSE} who_nrevss("national") who_nrevss("hhs") who_nrevss("census") who_nrevss("state") ``` ## 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.