example in README

.Rbuildignore

@@ -3,3 +3,5 @@ README.md
 Makefile
 ^.*\.Rproj$
 ^\.Rproj\.user$
+example.R
+nCov2019.png

Makefile

@@ -6,6 +6,10 @@ all: rd check clean
 
 alldocs: rd readme
 
+figure:
+	Rscript -e 'source("example.R")'
+
+
 rd:
 	Rscript -e 'library(methods); devtools::document()'
 # Rscript -e 'roxygen2::roxygenise(".")'

README.md

@@ -29,6 +29,11 @@ Get the development version from github:
 remotes::install_github("GuangchuangYu/nCov2019")
 ```
 
+## :art: Example
+
+Run the script [example.R](example.R) in R using `source("example.R")`, will produce the following figure:
+
+![](nCov2019.png)
 
 ## :book: Documents
 

example.R

@@ -0,0 +1,96 @@
+
+require(nCov2019)
+y <- load_nCov2019(lang = 'en', source='github')
+d = y['global']
+
+
+require(dplyr)
+dd <- filter(d, time == time(y)) %>% 
+    arrange(desc(cum_confirm)) 
+
+dd = dd[1:40, ]
+dd$country = factor(dd$country, levels=dd$country)
+
+dd$angle = 1:40 * 360/40
+require(ggplot2)
+p <- ggplot(dd, aes(country, cum_confirm, fill=cum_confirm)) + 
+    geom_col(width=1, color='grey90') + 
+    geom_col(aes(y=I(5)), width=1, fill='grey90', alpha = .2) +       
+    geom_col(aes(y=I(3)), width=1, fill='grey90', alpha = .2) +    
+    geom_col(aes(y=I(2)), width=1, fill = "white") +
+    scale_y_log10() + 
+    scale_fill_gradientn(colors=c("darkgreen", "green", "orange", "firebrick","red"), trans="log") + 
+    geom_text(aes(label=paste(country, cum_confirm, sep="\n"), 
+                  y = cum_confirm *.8, angle=angle), 
+            data=function(d) d[d$cum_confirm > 100,], 
+            size=3, color = "white", fontface="bold", vjust=1)  + 
+    geom_text(aes(label=paste0(cum_confirm, " cases ", country), 
+                  y = max(cum_confirm) * 2, angle=angle+90), 
+            data=function(d) d[d$cum_confirm < 100,], 
+            size=3, vjust=0) + 
+    coord_polar(direction=-1) + 
+    theme_void() + 
+    theme(legend.position="none") 
+
+p1 = ggplotify::as.ggplot(p, scale=1.45, vjust=-.15, hjust=.02)
+
+require(dplyr)
+require(ggplot2)
+require(shadowtext)
+require(nCov2019)
+
+d <- load_nCov2019()
+dd <- d['global'] %>% 
+  as_tibble %>%
+  rename(confirm=cum_confirm) %>%
+  filter(confirm > 100 & country != "China") %>%
+  group_by(country) %>%
+  mutate(days_since_100 = as.numeric(time - min(time))) %>%
+  ungroup 
+
+
+
+
+breaks=c(100, 200, 500, 1000, 2000, 5000, 10000, 20000, 50000, 100000)
+
+
+p2 <- ggplot(dd, aes(days_since_100, confirm, color = country)) +
+  geom_smooth(method='lm', aes(group=1),
+              data = . %>% filter(!country %in% c("Japan", "Singapore")), 
+              color='grey10', linetype='dashed') +
+  geom_line(size = 0.8) +
+  geom_point(pch = 21, size = 1) +
+  scale_y_log10(expand = expansion(add = c(0,0.1)), 
+                breaks = breaks, labels = breaks) +
+  scale_x_continuous(expand = expansion(add = c(0,1))) +
+  theme_minimal(base_size = 14) +
+  theme(
+    panel.grid.minor = element_blank(),
+    legend.position = "none",
+    plot.margin = margin(3,20,3,3,"mm")
+  ) +
+  coord_cartesian(clip = "off") +
+  geom_shadowtext(aes(label = paste0(" ",country)), hjust=0, vjust = 0, 
+                  data = . %>% group_by(country) %>% top_n(1, days_since_100), 
+                  bg.color = "white") +
+  labs(x = "Number of days since 100th case", y = NULL, 
+       title = "Confirmed COVID-19 cases",
+       subtitle = time(d))
+
+
+library(chinamap)
+
+x <- get_nCov2019(lang = 'en')
+cn = get_map_china()
+cn$province <- trans_province(cn$province)
+p3 <- plot(x, region = 'china', chinamap = cn,
+     continuous_scale = FALSE,
+     palette = 'Blues', font.size = 2) +
+     theme_minimal(base_size=14)
+
+require(cowplot)
+pp <- plot_grid(p2, p3, ncol=1, labels=c("B", "C"), 
+    rel_heights=c(.7, 1)) 
+g <- plot_grid(p1, pp, ncol=2, rel_widths=c(1.2, 1), labels=c("A", "")) 
+ggsave(g, filename = "nCov2019.png", width=16, height=11)
+