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

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

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

## What's Inside The Tin

The following functions are implemented:

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

## Installation

```{r install-ex, results='asis', echo=FALSE, cache=FALSE}
hrbrpkghelpr::install_block()
```

## Usage

```{r lib-ex}
library(cdccovidview)

# current version
packageVersion("cdccovidview")

```

```{r ex-01, fig.width = 10, fig.height = 7, cache=TRUE}
library(cdccovidview)
library(hrbrthemes)
library(tidyverse)

hosp <- laboratory_confirmed_hospitalizations()

hosp

c(
  "0-4 yr", "5-17 yr", "18-49 yr", "50-64 yr", "65+ yr", "65-74 yr", "75-84 yr", "85+"
) -> age_f

mutate(hosp, start = mmwr_week_to_date(mmwr_year, mmwr_week)) %>% 
  filter(!is.na(weekly_rate)) %>% 
  filter(catchment == "Entire Network") %>% 
  select(start, network, age_category, weekly_rate) %>%  
  filter(age_category != "Overall") %>% 
  mutate(age_category = factor(age_category, levels = age_f)) %>% 
  ggplot() +
  geom_line(
    aes(start, weekly_rate)
  ) +
  scale_x_date(
    date_breaks = "2 weeks", date_labels = "%b\n%d"
  ) +
  facet_grid(network~age_category) +
  labs(
    x = NULL, y = "Rates per 100,000 pop",
    title = "COVID-NET Weekly Rates by Network and Age Group",
    caption = sprintf("Source: COVID-NET: COVID-19-Associated Hospitalization Surveillance Network, Centers for Disease Control and Prevention.\n<https://gis.cdc.gov/grasp/COVIDNet/COVID19_3.html>; Accessed on %s", Sys.Date())
  ) +
  theme_ipsum_es(grid="XY")

```

### Clinical Labs

```{r ex-02}
head(clinical_labs())
```

### Public Health Labs

```{r ex-03}
head(public_health_labs_national())

head(public_health_labs_regional())
```

### Emergency Department Visits

```{r ex-04}
head(nssp_er_visits_national())

head(nssp_er_visits_regional())
```

### Mortality

```{r ex-05}
head(mortality_surveillance_data())
```

```{r ex-06}
pd <- provisional_death_counts()

head(pd$by_week)

head(pd$by_age)

head(pd$by_state)

head(pd$by_sex)
```

## cdccovidview Metrics

```{r cloc, 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.