pandemic.Rmd

---
title: "pandemic"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

- [Coronavirus: Why You Must Act Now (2020) Tomas Pueyo](https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca)
- [CSSE JHU COVID-19 Time series](https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series)

```{r message=FALSE}
library(dplyr)
library(tidyr)
library(ggplot2)
library(stringr)
library(readr)
library(RCurl)
```

```{r}
dirpath <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series"
cases_state <- bind_rows(
  confirm = read_csv(
    getURL(file.path(dirpath, "time_series_19-covid-Confirmed.csv"))),
  dead = read_csv(
    getURL(file.path(dirpath, "time_series_19-covid-Deaths.csv"))),
  recover = read_csv(
    getURL(file.path(dirpath, "time_series_19-covid-Recovered.csv"))),
  .id = "Type") %>%
  rename(State = "Province/State",
         Region = "Country/Region") %>%
  pivot_longer(-(Type:Long), names_to = "Date", values_to = "Count") %>%
  mutate(Date = as.POSIXct(Date, format="%m/%d/%y")) %>%
  mutate(State = ifelse(str_detect(State, ","), str_remove(State, "^.*, "), State),
         State = ifelse(State %in% state.name, 
                        state.abb[match(State, state.name)], 
                        State)) %>%
  group_by(Type, State, Region, Date) %>%
  summarize(Count = sum(Count)) %>%
  ungroup
  
cases <- cases_state %>%
  group_by(Type, Region, Date) %>%
  summarize(Count = sum(Count)) %>%
  ungroup
```

### Confirmed Cases

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  theme(legend.position = "none") +
  ggtitle("China confirmed cases")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("China confirmed cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0)) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("All Countries confirmed cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, Region != "China")) +
  aes(Date, Count, col = Region) +
  geom_line() +
  theme(legend.position = "none") +
  ggtitle("All Countries but China confirmed cases")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, Region == "US")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("US confirmed cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, 
                Region %in% c("Italy","Iran","Korea, South"))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  ggtitle("Italy, Iran, South Korea confirmed cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "confirm", Count > 0, 
                !(Region %in% c("US", "China", "Italy","Iran","Korea, South")))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("All but China, US, Italy, Iran, South Korea confirmed cases (geometric scale)")
```

```{r}
ggplot(cases_state %>% 
         filter(Type == "confirm", Count > 0, 
                Region == "US")) +
  aes(Date, Count, col = State) +
  geom_line() +
  scale_y_log10() +
#  theme(legend.position = "none") +
  ggtitle("US states confirmed cases (geometric scale)")
```

### Deaths

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  theme(legend.position = "none") +
  ggtitle("China deaths")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("China deaths (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0)) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  ggtitle("All Countries deaths (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, Region != "China")) +
  aes(Date, Count, col = Region) +
  geom_line() +
  ggtitle("All Countries but China deaths")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, Region == "US")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  ggtitle("US deaths (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, 
                Region %in% c("Italy","Iran","Korea, South"))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  ggtitle("Italy, Iran, South Korea deaths (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "dead", Count > 0, 
                !(Region %in% c("US", "China", "Italy","Iran","Korea, South")))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  ggtitle("All but China, US, Italy, Iran, South Korea deaths (geometric scale)")
```

```{r}
ggplot(cases_state %>% 
         filter(Type == "dead", Count > 0, 
                Region == "US")) +
  aes(Date, Count, col = State) +
  geom_line() +
  scale_y_log10() +
#  theme(legend.position = "none") +
  ggtitle("US states deaths (geometric scale)")
```

### Recovered cases

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  theme(legend.position = "none") +
  ggtitle("China recovered cases")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, Region == "China")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("China recovered cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0)) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("All Countries recovered cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, Region != "China")) +
  aes(Date, Count, col = Region) +
  geom_line() +
  theme(legend.position = "none") +
  ggtitle("All Countries but China recovered cases")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, Region == "US")) +
  aes(Date, Count) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("US recovered cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, 
                Region %in% c("Italy","Iran","Korea, South"))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  ggtitle("Italy, Iran, South Korea recovered cases (geometric scale)")
```

```{r}
ggplot(cases %>% 
         filter(Type == "recover", Count > 0, 
                !(Region %in% c("US", "China", "Italy","Iran","Korea, South")))) +
  aes(Date, Count, col = Region) +
  geom_line() +
  scale_y_log10() +
  theme(legend.position = "none") +
  ggtitle("All but China, US, Italy, Iran, South Korea recovered cases (geometric scale)")
```

```{r}
ggplot(cases_state %>% 
         filter(Type == "recover", Count > 0, 
                Region == "US")) +
  aes(Date, Count, col = State) +
  geom_line() +
  scale_y_log10() +
#  theme(legend.position = "none") +
  ggtitle("US states recovered cases (geometric scale)")
```