---
title: "Covid19 Chile"
output:
flexdashboard::flex_dashboard:
source_code: embed
orientation: columns
vertical_layout: fill
theme: flatly
---
```{r setup, include=FALSE}
library(flexdashboard)
library(tidyverse)
library(highcharter)
library(DT)
corona_cases<-read.csv("https://covid.ourworldindata.org/data/owid-covid-data.csv", header = TRUE, sep = ",")
population<-read.csv("https://covid.ourworldindata.org/data/ecdc/locations.csv", header = TRUE, sep = ",")
corona_total<-merge(population, corona_cases, by = "location")
corona_total<-filter(corona_total, corona_total$total_cases >= 1|corona_total$total_deaths >=1)
corona_total<-mutate(corona_total,
incidenciaX1000 = corona_total$new_cases/corona_total$population * 1000,
mortalidadX1000 = corona_total$new_deaths/corona_total$population * 1000,
incidenciaX1000000 = corona_total$total_cases/corona_total$population * 1000000,
mortalidadX1000000 = corona_total$total_deaths/corona_total$population * 1000000,
letalidad = corona_total$new_deaths/corona_total$new_cases * 100,
letalidad_acumulada = corona_total$total_deaths/corona_total$total_cases * 100,
total_cases_log = log10(corona_total$total_cases)
)
target<-c("United States",
"Italy",
"Argentina",
"Brazil",
"Bolivia",
"Colombia",
"Ecuador",
"Paraguay",
"Peru",
"Uruguay",
"Venezuela",
"Germany",
"France",
"Spain",
"China",
"South Korea",
"Japan"
)
target2<-c("Chile")
target3<-c("United States",
"Italy",
"Argentina",
"Brazil",
"Bolivia",
"Colombia",
"Ecuador",
"Paraguay",
"Peru",
"Uruguay",
"Venezuela",
"Germany",
"France",
"Spain",
"China",
"South Korea",
"Japan",
"Chile")
corona_dinamic_graph<-filter(corona_total, corona_total$location %in% target)
corona_dinamic_graph2<-filter(corona_total, corona_total$location %in% target2)
corona_table<-filter(corona_total, corona_total$location %in% target3)
corona_dinamic_graph<-arrange(corona_dinamic_graph, corona_dinamic_graph$date)
corona_dinamic_graph2<-arrange(corona_dinamic_graph2, corona_dinamic_graph2$date)
corona_dinamic_graph<-mutate(corona_dinamic_graph, new_date = as.Date(corona_dinamic_graph$date))
corona_dinamic_graph2<-mutate(corona_dinamic_graph2, new_date = as.Date(corona_dinamic_graph2$date))
total_casos_chile<-max(corona_dinamic_graph2$total_cases, na.rm = TRUE)
total_muertes_chile<-max(corona_dinamic_graph2$total_deaths, na.rm = TRUE)
total_test_chile<-max(corona_dinamic_graph2$total_tests, na.rm = TRUE)
incidencia_chile<-round(last(corona_dinamic_graph2$incidenciaX1000000), 1)
mortalidad_chile<-round(last(corona_dinamic_graph2$mortalidadX1000000), 1)
letalidad_chile<-round(last(corona_dinamic_graph2$letalidad_acumulada), 1)
chile_totales_nacionales<-read.csv("https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto5/TotalesNacionales.csv", header = TRUE, sep = ",", check.names = TRUE)
recuperados<-chile_totales_nacionales[3,ncol(chile_totales_nacionales)]
activos<-chile_totales_nacionales[5,ncol(chile_totales_nacionales)]
corona_cases_chile<-read.csv("https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto3/CasosTotalesCumulativo.csv", header = TRUE, sep = ",")
mapdata<-get_data_from_map(download_map_data("countries/cl/cl-all"))
mapdata<-mutate(mapdata, region_codigo = mapdata$`hc-a2`)
regiones<-data.frame("region_codigo"=c("AY", "TA", "AN", "AT", "CO", "VS", "RM", "LI", "ML", "ML","BI", "LA", "AR", "LL", "AI", "MA", "TO"))
corona_cases_chile<-cbind(corona_cases_chile, regiones)
mapdata<-merge(corona_cases_chile, mapdata, by = "region_codigo")
data_fake <- mapdata %>%
select(code = region_codigo) %>%
mutate(value = mapdata$X2020.04.23)
```
Home
=====================================
Column
-------------------------------------
### Chile
```{r plots, echo=FALSE}
hcmap("countries/cl/cl-all", data = data_fake, value = "value",
joinBy = c("hc-a2", "code"), name = "Casos por Región",
dataLabels = list(enabled = TRUE, format = '{point.name}'),
borderColor = "#0048BA", borderWidth = 1, tooltip = list(valueDecimals = 0, valuePrefix = "Casos Totales = "))
```
Column
-------------------------------------
### Casos Totales en Chile
```{r}
articles <- total_casos_chile
valueBox(articles, icon = "body")
```
### Casos Recuperados a la Fecha
```{r}
recu <- recuperados
valueBox(recu, icon = "body")
```
### Incidencia por Millón de Habitantes
```{r}
comments <- incidencia_chile
valueBox(comments, icon = "fas fa-skull-crossbones")
```
Column
-------------------------------------
### Muertes Totales en Chile
```{r}
comments <- total_muertes_chile
valueBox(comments, icon = "fas fa-skull-crossbones")
```
### Casos Activos a la Fecha
```{r}
activ <- activos
valueBox(activ, icon = "body")
```
### Mortalidad por Millón de Habitantes
```{r}
spam <- mortalidad_chile
valueBox(spam,
icon = "flask-sharp",
color = ifelse(spam > 10, "warning", "primary"))
```
Column
-------------------------------------
### Test Totales en Chile
```{r}
spam <-total_test_chile
valueBox(spam,
icon = "flask-sharp")
```
### Letalidad
```{r}
rate <- letalidad_chile
gauge(rate, min = 0, max = 100, symbol = '%', gaugeSectors(
success = c(0, 5), warning = c(6, 20), danger = c(21, 100)
))
```
Letalidad Acumulada a lo largo de la pandemia
Casos {data-navmenu="Diarios"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"column",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$new_cases,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"column",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$new_cases,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Casos Nuevos de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Nuevos casos"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Muertes {data-navmenu="Diarios"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"column",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$new_deaths,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"column",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$new_deaths,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Nuevas Muertes de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Nuevos casos"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Lineal {data-navmenu="Casos Totales"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$total_cases,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$total_cases,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Casos Totales de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Casos Totales"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Logarítmico {data-navmenu="Casos Totales"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$total_cases,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$total_cases,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Casos Totales de COVID19 por día de infección (escala logarítmica") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Casos Totales"),opposite = FALSE, type = "logarithmic") %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Lineal {data-navmenu="Muertes Totales"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$total_deaths,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$total_deaths,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Muertes Totales de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Muertes Totales"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Logarítmico {data-navmenu="Muertes Totales"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$total_deaths,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$total_deaths,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Muertes Totales de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Muertes totales"),opposite = FALSE, type = "logarithmic") %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Gráfico {data-navmenu="Incidencia"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$incidenciaX1000000,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$incidenciaX1000000,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Incidencia de COVID19 por día de infección por millón de habitantes") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Incidencia"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Gráfico {data-navmenu="Mortalidad"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$mortalidadX1000000,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$mortalidadX1000000,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Mortalidad de COVID19 por día de infección por millón de habitantes") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Mortalidad"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Puntual {data-navmenu="Letalidad"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"column",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$letalidad,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"column",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$letalidad,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Letalidad (%) de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Letalidad (%)"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Acumulada {data-navmenu="Letalidad"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$letalidad_acumulada,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$letalidad_acumulada,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Letalidad Acumulada (%) de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Letalidad Acumulada (%)"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Diarios {data-navmenu="Test"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"column",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$new_tests,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"column",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$new_tests,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Nuevos Tests Realizados de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Nuevos Tests"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```
Totales {data-navmenu="Test"}
=====================================
```{r}
highchart() %>%
hc_add_series(corona_dinamic_graph2,
"spline",
hcaes(x = corona_dinamic_graph2$new_date,
y = corona_dinamic_graph2$total_tests,
group = corona_dinamic_graph2$location), visible = TRUE) %>%
hc_add_series(corona_dinamic_graph,
"spline",
hcaes(x = corona_dinamic_graph$new_date,
y = corona_dinamic_graph$total_tests,
group = corona_dinamic_graph$location), visible = FALSE) %>%
hc_add_theme(hc_theme_google()) %>%
hc_title(text = "Tests Acumulados de COVID19 por día de infección") %>%
hc_xAxis(title = list(text = "Día de la Infección"),opposite = FALSE, type = "datetime") %>%
hc_yAxis(title = list(text = "Tests Acumulados"),opposite = FALSE) %>%
hc_legend(title = list(text = "País"), align = "left", vertilAlign = "top", layout = "vertical", x = 0, y = 0)
```