---
title: "Coronavirus en Colombia"
author: "www.cdedatos.com"
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")
library(coronavirus)
data(coronavirus) # load data
# update_datasets() # update data if possible
# View(coronavirus) # see data
# max(coronavirus$date) # show maximum data

`%>%` <- magrittr::`%>%`
#------------------ Parameters ------------------
# Set colors
# https://www.w3.org/TR/css-color-3/#svg-color
confirmed_color <- "#ffa726"
active_color <- "#009CBF"
recovered_color <- "forestgreen"
death_color <- "red"
#------------------ Data ------------------
# Here on df you create the dataframe of your desired country
df <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(Country.Region == "Colombia") %>%
  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))

# Here you create a dataframe with daily data for your country
df_daily <- coronavirus %>%
  dplyr::filter(Country.Region == "Colombia") %>%
  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)
  )

# the data for the lattest date
df1 <- coronavirus %>% dplyr::filter(date == max(date))
```

Línea de tiempo Colombia
=======================================================================

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

### confirmed {.value-box}

```{r}

valueBox(
  value = paste(format(sum(df$confirmed), big.mark = ","), "", sep = " "),
  caption = "Total de casos confirmados",
  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 = "Casos de muerte (índice de mortalidad)",
  icon = "fas fa-heart-broken",
  color = death_color
)
```


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

### **Casos diarios acumulados por tipo** (Solamente Colombia)
    
```{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 = "Confirmados",
    line = list(color = active_color),
    marker = list(color = active_color)
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~death_cum,
    type = "scatter",
    mode = "lines+markers",
    name = "Muertes",
    line = list(color = death_color),
    marker = list(color = death_color)
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-06"),
    y = 1,
    text = paste("Primer caso"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -10,
    ay = -90
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-22"),
    y = 3,
    text = paste("Primera muerte"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -5,
    ay = -50
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-17"),
    y = 80,
    text = paste(
      "Cierre de fronteras",
      " \n",
      "(terrestres, marítimas y fluviales)"
    ),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -90,
    ay = -120
  ) %>%
  plotly::layout(
    title = "",
    yaxis = list(title = "Número de casos acumulados"),
    xaxis = list(title = ""),
    legend = list(x = 0.1, y = 0.9),
    hovermode = "compare"
  )
```

Comparación
=======================================================================


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


### **Casos nuevos confirmados por día**
    
```{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 = ~Argentina, # país 1
    type = "scatter",
    mode = "lines+markers",
    name = "Argentina"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Brazil, # país 5
    type = "scatter",
    mode = "lines+markers",
    name = "Brasil"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Chile, # país 5
    type = "scatter",
    mode = "lines+markers",
    name = "Chile"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Colombia, # país 3
    type = "scatter",
    mode = "lines+markers",
    name = "Colombia"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Uruguay, # país 5
    type = "scatter",
    mode = "lines+markers",
    name = "Uruguay"
  ) %>%
  plotly::layout(
    title = "",
    legend = list(x = 0.1, y = 0.9),
    yaxis = list(title = "Número de casos nuevos"),
    xaxis = list(title = "Fecha"),
    # paper_bgcolor = "black",
    # plot_bgcolor = "black",
    # font = list(color = 'white'),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```
 
### **Distribución de muertes y casos confirmados **

```{r daily_summary}
df_EU <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(Country.Region == "Colombia" |
    Country.Region == "Argentina" |
    Country.Region == "Brazil" |
    Country.Region == "Chile" | 
    Country.Region == "Colombia" |
    Country.Region == "Uruguay") %>%
  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 = "Confirmados",
  marker = list(color = active_color)
) %>%
  plotly::add_trace(
    y = ~death,
    # text =  ~ death,
    # textposition = 'auto',
    name = "Muertes",
    marker = list(color = death_color)
  ) %>%
  plotly::layout(
    barmode = "stack",
    yaxis = list(title = "Casos totales"),
    xaxis = list(title = ""),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```


Mapa
=======================================================================

### **Mapa mundial de casos** (*use los íconos de + y - para hacer acercar y alejar*)

```{r}
# map tab added by Art Steinmetz
library(leaflet)
library(leafpop)
library(purrr)
cv_data_for_plot <- coronavirus %>%
  # dplyr::filter(Country.Region == "Belgium") %>%
  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)
  )
```





Acerca de
=======================================================================

**Tablero de datos del Coronavirus: el caso de Colombia**

Este tablero del Coronavirus: el caso de Colombia provee una visión general de la nueva epidemia coronavirus COVID-19 (2019-nCoV) para colombia y algunos países de Sudamérica. 

El tablero fue construído con R, usando el entorno de trabajo R Markdown y es una adaptación de [éste](https://ramikrispin.github.io/coronavirus_dashboard/){target="_blank"} elaborado por Rami Krispin.

**Código**

El código para elaborar su propia adaptación puede encontrarlo en  [GitHub](https://github.com/AntoineSoetewey/coronavirus_dashboard){target="_blank"}.

**Datos**

Los datos que alimentan este tablero es el conjunto de datos disponibles en  el paquete de datos de R [`{coronavirus}`](https://github.com/RamiKrispin/coronavirus){target="_blank"}. 
Asegúrese de descargar la versión de desarrollador del paquete para poder obtener una versión actualizada de los datos:

```
install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")
```
Los datos y el tablero los estaremos actualizando diariamente.

Los datos en bruto son obtenidos desde el [repositorio](https://github.com/RamiKrispin/coronavirus-csv){target="_blank"} del Centro de Sistemas, Ciencia e Ingeniería Coronavirus de la Universidad Johns Hopkins (JHU CCSE)   .

**Contacto**

Para obtener más información, [contáctenos](https://cdedatos.com/contact-conoce-mas-sobre-las-iniciativas-de-ciencia-de-datos/). 
Más información sobre el tablero puede encontrarse en este [artículo](https://www.statsandr.com/blog/how-to-create-a-simple-coronavirus-dashboard-specific-to-your-country-in-r/).

**Actualización**

Los datos son del `r format(max(coronavirus$date), "%A %B %d, %Y")` y el tablero fue actualizado el `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)*.