README.Rmd

---
output: rmarkdown::github_document
editor_options: 
  chunk_output_type: console
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```{r pkg-knitr-opts, include=FALSE}
hrbrpkghelpr::global_opts()
```

```{r badges, results='asis', echo=FALSE, cache=FALSE}
hrbrpkghelpr::stinking_badges()
```

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 Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal

## Description

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 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:

- `age_group_distribution`:	Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories
- `cdc_basemap`:	Retrieve CDC U.S. base maps
- `geographic_spread`:	State and Territorial Epidemiologists Reports of Geographic Spread of Influenza
- `get_weekly_flu_report`:	Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC
- `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 metadata 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

MMWR ID Utilities:

- `mmwrid_map`:	MMWR ID to Calendar Mappings
- `mmwr_week`:	Convert a Date to an MMWR day+week+year
- `mmwr_weekday`:	Convert a Date to an MMWR weekday
- `mmwr_week_to_date`:	Convert an MMWR year+week or year+week+day to a Date object

Deprecated functions:

- `get_flu_data`:	Retrieves state, regional or national influenza statistics from the CDC (deprecated)
- `get_hosp_data`:	Retrieves influenza hospitalization statistics from the CDC (deprecated)
- `get_state_data`:	Retrieves state/territory-level influenza statistics from the CDC (deprecated)

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)
- `mmwrid_map`:	MMWR ID to Calendar Mappings (it is exported & available, no need to use `data()`)

## Installation

```{r eval=FALSE}
# CRAN
install.packages("cdcfluview")

# main branch
remotes::install_git("https://git.rud.is/hrbrmstr/cdcfluview.git")
remotes::install_git("https://sr.ht/~hrbrmstr/cdcfluview")
remotes::install_git("https://gitlab.com/hrbrmstr/cdcfluview")
remotes::install_github("hrbrmstr/cdcfluview")
```

## Usage

```{r libs}
library(cdcfluview)
library(hrbrthemes)
library(tidyverse)

# current version
packageVersion("cdcfluview")
```

### Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories

```{r age-group-dist}
glimpse(age_group_distribution(years=2015))
```

### Retrieve CDC U.S. Coverage Map

```{r cdc-basemaps}
plot(cdc_basemap("national"))
plot(cdc_basemap("hhs"))
plot(cdc_basemap("census"))
plot(cdc_basemap("states"))
plot(cdc_basemap("spread"))
plot(cdc_basemap("surv"))
```

### State and Territorial Epidemiologists Reports of Geographic Spread of Influenza

```{r geographic-spread, message=FALSE, warning=FALSE}
glimpse(geographic_spread())
```

### Laboratory-Confirmed Influenza Hospitalizations

```{r surveillance-areas, fig.width=10, fig.height=7.5}
surveillance_areas()

glimpse(fs_nat <- hospitalizations("flusurv"))

ggplot(fs_nat, aes(wk_end, rate)) + 
  geom_line(aes(color=age_label, group=age_label)) +
  facet_wrap(~sea_description, scales="free_x") +
  scale_color_viridis_d(name=NULL) +
  labs(x=NULL, y="Rates per 100,000 population",
       title="FluSurv-NET :: Entire Network :: All Seasons :: Cumulative Rate") +
  theme_ipsum_rc()

glimpse(hospitalizations("eip", years=2015))

glimpse(hospitalizations("eip", "Colorado", years=2015))

glimpse(hospitalizations("ihsp", years=2015))

glimpse(hospitalizations("ihsp", "Oklahoma", years=2010))
```

### Retrieve ILINet Surveillance Data

```{r ili-df}
walk(c("national", "hhs", "census", "state"), ~{
  
  ili_df <- ilinet(region = .x)
  
  print(glimpse(ili_df))
  
  ggplot(ili_df, aes(week_start, unweighted_ili, group=region, color=region)) +
    geom_line() +
    viridis::scale_color_viridis(discrete=TRUE) +
    labs(x=NULL, y="Unweighted ILI", title=ili_df$region_type[1]) +
    theme_ipsum_rc(grid="XY") +
    theme(legend.position = "none") -> gg
  
  print(gg)
  
})
```

### Retrieve weekly state-level ILI indicators per-state for a given season

```{r ili-weekly-activity, fig.width=10, fig.height=5}
ili_weekly_activity_indicators(2017)

xdf <- map_df(2008:2017, ili_weekly_activity_indicators)

count(xdf, weekend, activity_level_label) %>% 
  complete(weekend, activity_level_label) %>% 
  ggplot(aes(weekend, activity_level_label, fill=n)) + 
  geom_tile(color="#c2c2c2", size=0.1) +
  scale_x_date(expand=c(0,0)) +
  viridis::scale_fill_viridis(name="# States", na.value="White") +
  labs(x=NULL, y=NULL, title="Weekly ILI Indicators (all states)") +
  coord_fixed(100/1) +
  theme_ipsum_rc(grid="") +
  theme(legend.position="bottom")
```

### Pneumonia and Influenza Mortality Surveillance

```{r nat-pi-mortality}
(nat_pi <- pi_mortality("national"))

select(nat_pi, week_end, percent_pni, baseline, threshold) %>% 
  gather(measure, value, -week_end) %>% 
  ggplot(aes(week_end, value)) + 
  geom_line(aes(group=measure, color=measure)) + 
  scale_y_percent() +
  scale_color_ipsum(name = NULL, labels=c("Baseline", "Percent P&I", "Threshold")) +
  labs(x=NULL, y="% of all deaths due to P&I",
       title="Percentage of all deaths due to pneumonia and influenza, National Summary") +
  theme_ipsum_rc(grid="XY") +
  theme(legend.position="bottom")

(st_pi <- pi_mortality("state", years=2015))

(reg_pi <- pi_mortality("region", years=2015))
```

### Retrieve metadata about U.S. State CDC Provider Data

```{r state-data-providers}
state_data_providers()
```

### Retrieve WHO/NREVSS Surveillance Data

```{r who-vrevss}
glimpse(xdat <- who_nrevss("national"))

mutate(xdat$combined_prior_to_2015_16, 
       percent_positive = percent_positive / 100) %>% 
  ggplot(aes(wk_date, percent_positive)) +
  geom_line() +
  scale_y_percent(name="% Positive") +
  labs(x=NULL, title="WHO/NREVSS Surveillance Data (National)") +
  theme_ipsum_rc(grid="XY")

who_nrevss("hhs", years=2016)

who_nrevss("census", years=2016)

who_nrevss("state", years=2016)
```

## cdcfluview Metrics

```{r echo=FALSE}
cloc::cloc_pkg_md()
```

## Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.