THE POWER

Data Science and technology Workshop Tirana 15&16 October 2021

Libraries

## First specify the packages of interest
packages = c("tidyverse", "sjlabelled","ggplot2","broom","GGally", "viridis", "janitor","lubridate","forecast","fpp3","quantmod","fpp2","ggthemes","hrbrthemes","correlation","see","ggraph","plotly","dplyr", "gganimate")

## Now load or install&load all
package.check <- lapply(
  packages,
  FUN = function(x) {
    if (!require(x, character.only = TRUE)) {
      install.packages(x, dependencies = TRUE)
      library(x, character.only = TRUE)
    }
  }
)

Data source

OWD<-read.csv("https://covid.ourworldindata.org/data/owid-covid-data.csv")
head(OWD)

Time variable

OWD$date<- as.POSIXct(OWD$date, format = "%Y-%m-%d")
OWD$date<-as.Date(OWD$date,format='%Y/%m/%d')# convert time date into a date variable
OWD<-OWD %>%
  dplyr::mutate(year = lubridate::year(date), 
                month = lubridate::month(date), 
                day = lubridate::day(date))
##  Convert numeric month numeric values to name abbreviations
OWD$month<- month.abb[OWD$month] 
## remove all empty variables (columns) from dataset (janitor package)
OWD<-OWD %>%
  remove_empty("cols") #select either row or cols or both
dim(OWD)# there are not empty columns

[1] 123539     68

# substitute negative values from columns with NA-s
OWD<-OWD
OWD[OWD<0] <- 0 

Plot time series

OWD.1<-OWD %>%
  dplyr::filter(location == "World")
fig <- plot_ly(OWD.1, x = ~date)
fig <- fig %>% add_lines(y = ~total_cases, name = "Total Cases")
fig <- fig %>% add_lines(y = ~total_deaths, name = "Total Deaths")
fig <- fig %>% layout(
    title = "Covid daily cumulative Cases and Deaths",
    xaxis = list(
      rangeselector = list(
        buttons = list(
          list(
            count = 3,
            label = "3 mo",
            step = "month",
            stepmode = "backward"),
          list(
            count = 6,
            label = "6 mo",
            step = "month",
            stepmode = "backward"),
          list(
            count = 1,
            label = "1 yr",
            step = "year",
            stepmode = "backward"),
          list(
            count = 1,
            label = "YTD",
            step = "year",
            stepmode = "todate"),
          list(step = "all"))),

      rangeslider = list(type = "date")),

    yaxis = list(title = "Number of Cases"))

fig

BoxPlot

OWD.2<-OWD %>%
 filter(continent %in% c("Europe", "North America","Asia","Africa","South America","Oceania"))
fig <- plot_ly(OWD.2, x = ~total_deaths, color = ~continent, type = "box")

fig

Warning: Ignoring 17296 observations
Warning: Ignoring 17296 observations

OWD.eu<-OWD %>%
 filter(continent %in% c("Europe"))

fig <- plot_ly(OWD.eu, type = 'scatter', mode = 'lines')%>%
  add_trace(x = ~date, y = ~people_vaccinated,color=~location)%>%
  layout(showlegend = F, title='Time Series of people vaccinated for Europe',
         xaxis = list(rangeslider = list(visible = T),
                      rangeselector=list(
                        buttons=list(
                          list(count=1, label="1m", step="month", stepmode="backward"),
                          list(count=6, label="6m", step="month", stepmode="backward"),
                          list(count=1, label="YTD", step="year", stepmode="todate"),
                          list(count=1, label="1y", step="year", stepmode="backward"),
                          list(step="all")
                        ))))
fig <- fig %>%
  layout(
         xaxis = list(zerolinecolor = '#ffff',
                      zerolinewidth = 2,
                      gridcolor = 'ffff'),
         yaxis = list(zerolinecolor = '#ffff',
                      zerolinewidth = 2,
                      gridcolor = 'ffff'),
         plot_bgcolor='#e5ecf6', margin = 0.1, width = 900)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

fig

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New cases dynamic evolution of Covid-19

library(gganimate)
OWD_1<-subset(OWD, location != "Asia")
OWD_1<-subset(OWD_1, location!="Europe")
OWD_1<-subset(OWD_1, location!="North America")
OWD_1<-subset(OWD_1, location!="South America")
OWD_1<-subset(OWD_1, location!="World")
OWD_1<-subset(OWD_1, location!="European Union")
OWD_1<-subset(OWD_1, location!="International")
OWD_1<-subset(OWD_1, location!="Oceania")
OWD_1<-subset(OWD_1, location!="Africa")

# OWD_1 has World and other location removed
OWD_4<-OWD_1 %>%
 filter(date >= as.Date("2021-09-01"))

p <- OWD_4 %>%
  filter(new_cases > 0 & new_cases < 40000000) %>%
  arrange(location, date) %>%
  group_by(location) %>%
  mutate(new_cases_cum = cumsum(new_cases)) %>%
  group_by(date) %>%
  top_n(10, new_cases_cum) %>%
  mutate(location = factor(location)) %>%
  mutate(rank = dense_rank(-new_cases_cum)) %>%
  ungroup %>%
  ggplot() + 
  aes(rank, group = location, fill = location, color = location) +
  geom_tile(aes(y = new_cases_cum/2,height = new_cases_cum, width = 0.9), alpha = 0.8, color = NA) + 
  geom_text(aes(y = 0, label = paste(location, " ")), vjust = 0.2, hjust = 1) +
  coord_flip(clip = "off", expand = FALSE) +
  scale_y_continuous(labels = scales::comma) +
  scale_x_reverse() +
  guides(color = FALSE, fill = FALSE) +
  labs(title='{closest_state}', x = "", y = "Total cases") +
  theme(plot.title = element_text(hjust = 0, size = 22),axis.ticks.y = element_blank(),axis.text.y  = element_blank(),plot.margin = margin(1,1,1,4, "cm"))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

p+transition_states(date, transition_length = 20)

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Total Vaccinations dynamic evolution of Covid-19

p <- OWD_4 %>%
  filter(total_vaccinations > 0 & total_vaccinations < 3400000000) %>%
  arrange(location, date) %>%
  group_by(location) %>%
  mutate(total_vaccinations_cum = cumsum(total_vaccinations)) %>%
  group_by(date) %>%
  top_n(10, total_vaccinations_cum) %>%
  mutate(location = factor(location)) %>%
  mutate(rank = dense_rank(-total_vaccinations_cum)) %>%
  ungroup %>%
  ggplot() + 
  aes(rank, group = location, fill = location, color = location) +
  geom_tile(aes(y = total_vaccinations_cum/2,height = total_vaccinations_cum, width = 0.9), alpha = 0.8, color = NA) + 
  geom_text(aes(y = 0, label = paste(location, " ")), vjust = 0.2, hjust = 1) +
  coord_flip(clip = "off", expand = FALSE) +
  scale_y_continuous(labels = scales::comma) +
  scale_x_reverse() +
  guides(color = FALSE, fill = FALSE) +
  labs(title='{closest_state}', x = "", y = "Total Vaccinations") +
  theme(plot.title = element_text(hjust = 0, size = 22),axis.ticks.y = element_blank(),axis.text.y  = element_blank(),plot.margin = margin(1,1,1,4, "cm"))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

p+transition_states(date, transition_length = 20)

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