---
title: "COVID-19 global"
output: 
  flexdashboard::flex_dashboard:
    theme: readable
    source_code: embed
    navbar:
      - { title: "Source: European Center for Disease Control (ECDC)", href: "https://www.ecdc.europa.eu/en/covid-19-pandemic", align: right }
---

```{r setup, include=FALSE}
library(flexdashboard)
library(lubridate)
library(forcats)
library(tidyverse)
library(ggplot2)
library(plotly)
```

Column
-----------------------------------------------------------------------

### Total COVID-19 cases per country

```{r}
# get latest data
# FROM: https://www.ecdc.europa.eu
data <- read.csv("https://opendata.ecdc.europa.eu/covid19/casedistribution/csv", na.strings = "", fileEncoding = "UTF-8-BOM", stringsAsFactors = F)
# convert date format
data$date_reported <- mdy(paste0(data$month,"-",data$day,"-",data$year))

# total cases and max single day by country
fig <- data %>%
 group_by(countriesAndTerritories) %>%
 summarise(cases_sum = sum(cases), cases_max = max(cases)) %>%
 mutate(countriesAndTerritories = fct_reorder(countriesAndTerritories, cases_sum)) %>%
  plot_ly(x = ~cases_sum,
          y = ~countriesAndTerritories,
          color = ~countriesAndTerritories,
          colors = 'Reds',
          type = "bar")
fig %>% layout(
         xaxis = list(title = "total cases"),
         yaxis = list(title = "country"))
fig

```

### Total COVID-19 cases and deaths (hover for more info)

```{r}
#build interactive global map 
df <- data %>% 
 group_by(countriesAndTerritories, countryterritoryCode) %>% 
 summarise(cases = sum(cases), deaths = sum(deaths))

df$hover <- with(df, paste(countriesAndTerritories, "
", "cases", cases, "
", "deaths", deaths))
l <- list(color = toRGB("grey"), width = 0.5)

g <- list(
  showframe = FALSE,
  showcoastlines = TRUE,
  projection = list(type = 'Mercator')
)

fig <- plot_geo(df) %>%
  add_trace(
    z = ~cases, color = ~cases, colors = 'Reds',
    text = ~hover, locations = ~countryterritoryCode, marker = list(line = l)
  ) %>%
  colorbar(title = 'confirmed cases') %>%
  layout(
    geo = g
  )

fig

```


Column 
-----------------------------------------------------------------------

### Daily COVID-19 cases in US

```{r}
# cases by date for US
us <- data[data$countriesAndTerritories == "United_States_of_America",]
fig <- plot_ly(us, 
               x = ~date_reported,
               y = ~cases, 
               type = "bar")
fig <- fig %>%layout(
         xaxis = list(title = "date"),
         yaxis = list(title = "cases"))
fig
       
# deaths by date for US
us <- data[data$countriesAndTerritories == "United_States_of_America",]
fig <- plot_ly(us, 
               x = ~date_reported,
               y = ~deaths, 
               type = "bar")
fig <- fig %>% layout(
         xaxis = list(title = "date"),
         yaxis = list(title = "deaths"))
fig
```

### Daily COVID-19 deaths in US

```{r}
     # deaths by date for US
us <- data[data$countriesAndTerritories == "United_States_of_America",]
fig <- plot_ly(us, 
               x = ~date_reported,
               y = ~deaths, 
               type = "bar")
fig <- fig %>% layout(
         xaxis = list(title = "date"),
         yaxis = list(title = "deaths"))
fig
```