COVID-19

Daily Reports

r03_24=subset(report_03_24,Country_Region == "US")
r03_24=r03_24[,-c(1,2,5,6,7,12)]
r03_24=group_by(r03_24, Province_State) %>% summarise(Confirmed=sum(Confirmed), Deaths=sum(Deaths), Recovered=sum(Recovered))

r03_24 %>%
    ggplot() +
    geom_point(aes(x = Confirmed, y = reorder(Province_State, Confirmed), color="blue")) +
    geom_point(aes(x = Deaths, y = reorder(Province_State, Deaths), color="red"))+
  scale_color_manual(values =c('red'='red','blue'='blue', 'purple'='purple'), labels = c('Confirmed',"Recovered", 'Deaths'))+ 
  scale_x_continuous(trans='log10')+
  xlab("Cases (log10)")+
  ylab("State")+
  ggtitle("American Cases as of 3-24-20")

## Warning: Transformation introduced infinite values in continuous x-axis

## Warning: Transformation introduced infinite values in continuous x-axis

mybreaks = c(1, 20, 100, 1000, 5000)

USmap <- map_data("usa")

us_03_24=report_03_24[!(report_03_24$Province_State %in% c("American Samoa" , "Northern Mariana Islands","Recovered", "Wuhan Evacuee", "Virgin Islands", "Grand Princess", "Guam", "Puerto Rico", "Diamond Princess")),]

us_03_24=subset(us_03_24,Country_Region == "US")
us_03_24=subset(us_03_24,Lat != 0)

ggplot() +
  geom_polygon(data = USmap, aes(x=long, y = lat, group = group), fill="grey", alpha=0.3) +
  geom_point(data=subset(us_03_24, Country_Region=="US"), aes(x=Long_, y=Lat,size=Confirmed, color=Confirmed),stroke=F, alpha=0.7) +
    scale_size_continuous(name="Cases", trans="log", range=c(1,7), breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-4,999", "5,000+")) +
  # scale_alpha_continuous(name="Cases", trans="log", range=c(0.1, 0.9),breaks=mybreaks) +
  scale_color_viridis_c(option="inferno",name="Cases", trans="log",breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-4,999", "5,000+")) +
  theme_void() + 
  guides( colour = guide_legend()) +
  labs(caption = "") +
  theme(
    legend.position = "bottom",
    text = element_text(color = "#22211d"),
    plot.background = element_rect(fill = "#ffffff", color = NA), 
    panel.background = element_rect(fill = "#ffffff", color = NA), 
    legend.background = element_rect(fill = "#ffffff", color = NA)
  )+
  ggtitle("Confirmed Cases in the US as of 3-24-20")

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning in sqrt(x): NaNs produced

## Warning: Removed 1785 rows containing missing values (geom_point).

Time Series

iran=full_join(time_series_deaths_long, time_series_recovered_long, by=c("Country.Region", "Date"))
iran=full_join(iran, time_series_confirmed_long, by=c("Country.Region", "Date"))

iran %>% 
  filter (Country.Region == "Iran") %>% 
    ggplot() + 
    geom_line(aes(x = Date, y = Confirmed, color = "blue"))+
    geom_line(aes(x = Date, y = Deaths, color = "red"))+
    geom_line(aes(x = Date, y = Recovered, color = "purple"))+
    ggtitle("Iran COVID-19 Cases")+
   ylab("Count")+
  scale_color_manual(values =c('red'='red','blue'='blue', 'purple'='purple'), labels = c('Confirmed',"Recovered", 'Deaths'))

## Warning: Removed 2 rows containing missing values (geom_path).

## Warning: Removed 2 rows containing missing values (geom_path).

iran=full_join(time_series_deaths_long, time_series_recovered_long, by=c("Country.Region", "Date"))
iran=full_join(iran, time_series_confirmed_long, by=c("Country.Region", "Date"))

iran %>% 
  filter (Country.Region == "Italy") %>% 
    ggplot() + 
    geom_line(aes(x = Date, y = Confirmed, color = "blue"))+
    geom_line(aes(x = Date, y = Deaths, color = "red"))+
    geom_line(aes(x = Date, y = Recovered, color = "purple"))+
    ggtitle("Italy COVID-19 Cases")+
   ylab("Count")+
  scale_color_manual(values =c('red'='red','blue'='blue', 'purple'='purple'), labels = c('Confirmed','Recovered', "Deaths"))

## Warning: Removed 2 rows containing missing values (geom_path).

## Warning: Removed 2 rows containing missing values (geom_path).

Maps

world <- map_data("world")
mybreaks <- c(1, 20, 100, 1000, 50000)

ggplot() +
  geom_polygon(data = world, aes(x=long, y = lat, group = group), fill="grey", alpha=0.3) +
  geom_point(data=time_series_deaths, aes(x=Long, y=Lat, size=`2/25/20`, color=`2/25/20`),stroke=F, alpha=0.7) +
  scale_size_continuous(name="Cases", trans="log", range=c(1,7), breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-49,999", "50,000+")) +
  # scale_alpha_continuous(name="Cases", trans="log", range=c(0.1, 0.9),breaks=mybreaks) +
  scale_color_viridis_c(option="inferno",name="Cases", trans="log",breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-49,999", "50,000+")) +
  theme_void() + 
  guides( colour = guide_legend()) +
  labs(caption = "") +
  theme(
    legend.position = "bottom",
    text = element_text(color = "#22211d"),
    plot.background = element_rect(fill = "#ffffff", color = NA), 
    panel.background = element_rect(fill = "#ffffff", color = NA), 
    legend.background = element_rect(fill = "#ffffff", color = NA)
  )+
  ggtitle("Worldwide Deaths")

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning in sqrt(x): NaNs produced

## Warning: Removed 467 rows containing missing values (geom_point).

ggplot() +
  geom_polygon(data = world, aes(x=long, y = lat, group = group), fill="grey", alpha=0.3) +
  geom_point(data=time_series_recovered, aes(x=Long, y=Lat, size=`2/25/20`, color=`2/25/20`),stroke=F, alpha=0.7) +
  scale_size_continuous(name="Cases", trans="log", range=c(1,7), breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-49,999", "50,000+")) +
  # scale_alpha_continuous(name="Cases", trans="log", range=c(0.1, 0.9),breaks=mybreaks) +
  scale_color_viridis_c(option="inferno",name="Cases", trans="log",breaks=mybreaks, labels = c("1-19", "20-99", "100-999", "1,000-49,999", "50,000+")) +
  theme_void() + 
  guides( colour = guide_legend()) +
  labs(caption = "") +
  theme(
    legend.position = "bottom",
    text = element_text(color = "#22211d"),
    plot.background = element_rect(fill = "#ffffff", color = NA), 
    panel.background = element_rect(fill = "#ffffff", color = NA), 
    legend.background = element_rect(fill = "#ffffff", color = NA)
  )+
  ggtitle("Worldwide Recovery")

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning: Transformation introduced infinite values in discrete y-axis

## Warning in sqrt(x): NaNs produced

## Warning: Removed 437 rows containing missing values (geom_point).

COVID-19

Arianna Kazemi

3/25/2020

Daily Reports

Time Series

Maps