A-county-charts.Rmd

---
font: Lato
fontsize: 10pt
geometry: left=1in,right=1in,top=0.35in,bottom=0.6in
header-includes: \input{preamble.tex}
output:
  pdf_document: default
  word_document: 
  html_document:
sansfont: Lato
urlcolor: null
params:
  county: "Los Angeles"
  start_date: "2020-04-15"
---

\raggedright


```{r rmarkdown-setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(dev = "cairo_pdf")
options(knitr.kable.NA = "")
options(kableExtra.latex.load_packages = FALSE)

# Knit RMarkdown
library(knitr)

# Tables
library(kableExtra)

# Data Cleaning pipeline
library(tidyverse)
library(dplyr)
library(scales) # formatting numbers
library(arrow) # read parquets
library(zoo) # moving averages
library(reshape2)
library(aws.s3)


# Plotting
library(ggplot2)
library(ggthemes)
```


```{r import-data, echo=FALSE}
us_county<-arrow::read_parquet("../data/us-county-time-series.parquet", as_tibble=TRUE)
ca_hospitalizations<-read.csv("https://raw.githubusercontent.com/CityOfLosAngeles/covid19-indicators/master/data/ca-hospital-and-surge-capacity.csv")

# Call parameters from our utils files
source("../notebooks/r_utils.R")
YESTERDAY_DATE <-YESTERDAY_DATE
TWO_WEEKS_AGO <- TWO_WEEKS_AGO


# Call parameters from utils files
source("../notebooks/r_chart_utils.R")
# Chart parameters
NAVY<-NAVY
MAROON<- MAROON
LIGHT_GRAY<-LIGHT_GRAY
```


```{r select-parameter, echo = FALSE}

source("../notebooks/r_utils.R")

cases <- prep_county(us_county, params$county, params$start_date)

hospitalizations <-prep_hospital(ca_hospitalizations, params$county, params$start_date)

```



\clatitle{Daily Coronavirus Report}
\clasubtitle{Report by: Tiffany Chu}

## `r {params$county}` County: COVID-19 Trends


```{r get-caption, echo = FALSE}

subset_df <-cases %>% 
  subset(date ==YESTERDAY_DATE) %>%
  select(c("date", "cases", "deaths"))

```

As of `r YESTERDAY_DATE`, there have been `r comma(subset_df$cases)` cumulative cases and `r comma(subset_df$deaths)` cumulative deaths in `r params$county` County.



```{r charts,echo=FALSE, fig.align="left", fig.show="hold", out.width=c("70%", "70%")}

source("../notebooks/r_chart_utils.R")

# Plot cases / deaths

cases_chart<-plotCasesDeaths(cases, y_var=new_cases_avg7, 
                line_color=NAVY, 
                # params$county won't evaluate here, so instead, grab from the df
                chart_title=paste(cases$county[1], "County: New Cases"), 
                ytitle="daily new cases")

deaths_chart<-plotCasesDeaths(cases, y_var=new_deaths_avg7, 
                line_color=MAROON, 
                chart_title=paste(cases$county[1], "County: New Deaths"), 
                ytitle="daily new deaths")
```

\clafigurenumber{1}
\clafiguretitle{figure title!}

```{r cases-chart,echo=FALSE, fig.align="left", fig.show="hold", out.width="50%"}

cases_chart
```

\clasource{Johns Hopkins University}


\clafigurenumber{2}

```{r deaths-chart,echo=FALSE, fig.align="left", fig.show="hold", out.width="50%"}

deaths_chart
```



\contactinfo{}