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title: ""
pagetitle: ""
output: rmarkdown::github_document
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# 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:

- `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.