---
title: "Coronavirus in Portugal"
author: "Tiago A. Marques"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    # social: ["facebook", "twitter", "linkedin"]
    source_code: embed
    vertical_layout: fill
---

```{r setup, include=FALSE}
#------------------ Packages ------------------
library(flexdashboard)
# install.packages("devtools")
#devtools::install_github("RamiKrispin/coronavirus", force = TRUE)
library(coronavirus)
data(coronavirus)
# update_datasets()
# View(coronavirus)
# max(coronavirus$date)

`%>%` <- magrittr::`%>%`
#------------------ Parameters ------------------
# Set colors
# https://www.w3.org/TR/css-color-3/#svg-color
confirmed_color <- "purple"
active_color <- "#1f77b4"
recovered_color <- "forestgreen"
death_color <- "red"
#------------------ Data ------------------
df <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(Country.Region == "Portugal") %>%
  dplyr::group_by(Country.Region, type) %>%
  dplyr::summarise(total = sum(cases)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  # dplyr::mutate(unrecovered = confirmed - ifelse(is.na(recovered), 0, recovered) - ifelse(is.na(death), 0, death)) %>%
  dplyr::mutate(unrecovered = confirmed - ifelse(is.na(death), 0, death)) %>%
  dplyr::arrange(-confirmed) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(country = dplyr::if_else(Country.Region == "United Arab Emirates", "UAE", Country.Region)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "Mainland China", "China", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "North Macedonia", "N.Macedonia", country)) %>%
  dplyr::mutate(country = trimws(country)) %>%
  dplyr::mutate(country = factor(country, levels = country))

df_daily <- coronavirus %>%
  dplyr::filter(Country.Region == "Portugal") %>%
  dplyr::group_by(date, type) %>%
  dplyr::summarise(total = sum(cases, na.rm = TRUE)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  dplyr::arrange(date) %>%
  dplyr::ungroup() %>%
  #dplyr::mutate(active = confirmed - death - recovered) %>%
  dplyr::mutate(active = confirmed - death) %>%
  dplyr::mutate(
    confirmed_cum = cumsum(confirmed),
    death_cum = cumsum(death),
    # recovered_cum = cumsum(recovered),
    active_cum = cumsum(active)
  )


df1 <- coronavirus %>% dplyr::filter(date == max(date))
```

Summary
=======================================================================

Row {data-width=400}
-----------------------------------------------------------------------

### confirmed {.value-box}

```{r}

valueBox(
  value = paste(format(sum(df$confirmed), big.mark = ","), "", sep = " "),
  caption = "Total confirmed cases",
  icon = "fas fa-user-md",
  color = confirmed_color
)
```
















### death {.value-box}

```{r}

valueBox(
  value = paste(format(sum(df$death, na.rm = TRUE), big.mark = ","), " (",
    round(100 * sum(df$death, na.rm = TRUE) / sum(df$confirmed), 1),
    "%)",
    sep = ""
  ),
  caption = "Death cases (death rate)",
  icon = "fas fa-heart-broken",
  color = death_color
)
```


Row
-----------------------------------------------------------------------

### **Daily cumulative cases by type** (Portugal only)
    
```{r}
plotly::plot_ly(data = df_daily) %>%
  plotly::add_trace(
    x = ~date,
    # y = ~active_cum,
    y = ~confirmed_cum,
    type = "scatter",
    mode = "lines+markers",
    # name = "Active",
    name = "Confirmed",
    line = list(color = active_color),
    marker = list(color = active_color)
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~death_cum,
    type = "scatter",
    mode = "lines+markers",
    name = "Death",
    line = list(color = death_color),
    marker = list(color = death_color)
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-02"),
    y = 1,
    text = paste("First case"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -10,
    ay = -90
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-16"),
    y = 5,
    text = paste("Schools close"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -110,
    ay = -120
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-17"),
    y = 14,
    text = paste("First death"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -10,
    ay = -190
  ) %>%
  plotly::layout(
    title = "",
    yaxis = list(title = "Cumulative number of cases"),
    xaxis = list(title = "Date"),
    legend = list(x = 0.1, y = 0.9),
    hovermode = "compare"
  )
```

Comparison
=======================================================================


Column {data-width=400}
-------------------------------------


### **Daily new cases**
    
```{r}
daily_confirmed <- coronavirus %>%
  dplyr::filter(type == "confirmed") %>%
  dplyr::filter(date >= "2020-02-29") %>%
  dplyr::mutate(country = Country.Region) %>%
  dplyr::group_by(date, country) %>%
  dplyr::summarise(total = sum(cases)) %>%
  dplyr::ungroup() %>%
  tidyr::pivot_wider(names_from = country, values_from = total)

#----------------------------------------
# Plotting the data

daily_confirmed %>%
  plotly::plot_ly() %>%
  plotly::add_trace(
    x = ~date,
    y = ~Portugal,
    type = "scatter",
    mode = "lines+markers",
    name = "Portugal"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~France,
    type = "scatter",
    mode = "lines+markers",
    name = "France"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Spain,
    type = "scatter",
    mode = "lines+markers",
    name = "Spain"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Italy,
    type = "scatter",
    mode = "lines+markers",
    name = "Italy"
  ) %>%
   plotly::add_trace(
    x = ~date,
    y = ~US,
    type = "scatter",
    mode = "lines+markers",
    name = "US"
  ) %>%
   plotly::add_trace(
    x = ~date,
    y = ~`United Kingdom`,
    type = "scatter",
    mode = "lines+markers",
    name = "United Kingdom"
  ) %>%
  plotly::layout(
    title = "",
    legend = list(x = 0.1, y = 0.9),
    yaxis = list(title = "Number of new cases"),
    xaxis = list(title = "Date"),
    # paper_bgcolor = "black",
    # plot_bgcolor = "black",
    # font = list(color = 'white'),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```
 
### **Cases distribution by type**

```{r daily_summary}
df_EU <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(Country.Region == "Portugal" |
    Country.Region == "France" |
    Country.Region == "Italy" |
    Country.Region == "Spain" |
    Country.Region == "United Kingdom" |
    Country.Region == "US"  ) %>%
  dplyr::group_by(Country.Region, type) %>%
  dplyr::summarise(total = sum(cases)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  # dplyr::mutate(unrecovered = confirmed - ifelse(is.na(recovered), 0, recovered) - ifelse(is.na(death), 0, death)) %>%
  dplyr::mutate(unrecovered = confirmed - ifelse(is.na(death), 0, death)) %>%
  dplyr::arrange(confirmed) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(country = dplyr::if_else(Country.Region == "United Arab Emirates", "UAE", Country.Region)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "Mainland China", "China", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "North Macedonia", "N.Macedonia", country)) %>%
  dplyr::mutate(country = trimws(country)) %>%
  dplyr::mutate(country = factor(country, levels = country))

plotly::plot_ly(
  data = df_EU,
  x = ~country,
  # y = ~unrecovered,
  y = ~ confirmed,
  # text =  ~ confirmed,
  # textposition = 'auto',
  type = "bar",
  name = "Confirmed",
  marker = list(color = active_color)
) %>%
  plotly::add_trace(
    y = ~death,
    # text =  ~ death,
    # textposition = 'auto',
    name = "Death",
    marker = list(color = death_color)
  ) %>%
  plotly::layout(
    barmode = "stack",
    yaxis = list(title = "Total cases"),
    xaxis = list(title = ""),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```


Map
=======================================================================

### **World map of cases** (*use + and - icons to zoom in/out*)

```{r}
# map tab added by Art Steinmetz
library(leaflet)
library(leafpop)
library(purrr)
cv_data_for_plot <- coronavirus %>%
  # dplyr::filter(Country.Region == "Portugal") %>%
  dplyr::filter(cases > 0) %>%
  dplyr::group_by(Country.Region, Province.State, Lat, Long, type) %>%
  dplyr::summarise(cases = sum(cases)) %>%
  dplyr::mutate(log_cases = 2 * log(cases)) %>%
  dplyr::ungroup()
cv_data_for_plot.split <- cv_data_for_plot %>% split(cv_data_for_plot$type)
pal <- colorFactor(c("orange", "red", "green"), domain = c("confirmed", "death", "recovered"))
map_object <- leaflet() %>% addProviderTiles(providers$Stamen.Toner)
names(cv_data_for_plot.split) %>%
  purrr::walk(function(df) {
    map_object <<- map_object %>%
      addCircleMarkers(
        data = cv_data_for_plot.split[[df]],
        lng = ~Long, lat = ~Lat,
        #                 label=~as.character(cases),
        color = ~ pal(type),
        stroke = FALSE,
        fillOpacity = 0.8,
        radius = ~log_cases,
        popup = leafpop::popupTable(cv_data_for_plot.split[[df]],
          feature.id = FALSE,
          row.numbers = FALSE,
          zcol = c("type", "cases", "Country.Region", "Province.State")
        ),
        group = df,
        #                 clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F),
        labelOptions = labelOptions(
          noHide = F,
          direction = "auto"
        )
      )
  })

map_object %>%
  addLayersControl(
    overlayGroups = names(cv_data_for_plot.split),
    options = layersControlOptions(collapsed = FALSE)
  )
```





About
=======================================================================

**The Coronavirus Dashboard: the case of Portugal**

This Coronavirus dashboard: the case of Portugal provides an overview of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic for Portugal. This dashboard is built with R using the R Makrdown framework and was adapted from this [dashboard](https://ramikrispin.github.io/coronavirus_dashboard/){target="_blank"} by Rami Krispin.

This was adapted by Tiago A. Marques for Portugal after reading Antoine Soetewey blog post here:

https://www.statsandr.com/blog/how-to-create-a-simple-coronavirus-dashboard-specific-to-your-country-in-r/

A really outstanding resource, so many thanks Antoine!

**Code**

The code behind this dashboard is available on [GitHub](https://github.com/AntoineSoetewey/coronavirus_dashboard){target="_blank"}.

**Data**

The input data for this dashboard is the dataset available from the [`{coronavirus}`](https://github.com/RamiKrispin/coronavirus){target="_blank"} R package. Make sure to download the development version of the package to have the latest data:

```
install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")
```

The data and dashboard are refreshed on a daily basis.

The raw data is pulled from the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus [repository](https://github.com/RamiKrispin/coronavirus-csv){target="_blank"}.

Note that I suspect there is an error in the data at the JH repository. No new cases are reported for March 18th, so value of total cases is the same as for 17th March (448) when it should be 642.

**Contact**

For any question or feedback, you can contact the person I blatantly stole this code from [Antoine Soetewey](https://www.statsandr.com/contact/). More information about this dashboard can be found in this [article](https://www.statsandr.com/blog/how-to-create-a-simple-coronavirus-dashboard-specific-to-your-country-in-r/).

**Update**

The data is as of `r format(max(coronavirus$date), "%A %B %d, %Y")` and the dashboard has been updated on `r format(Sys.time(), "%A %B %d, %Y")`.



*Go back to [www.statsandr.com](https://www.statsandr.com/) (blog) or [www.antoinesoetewey.com](https://www.antoinesoetewey.com/) (personal website)*.