Hands-on Exercise 4c

Author

Lennis

Published

May 5, 2023

Getting Started

Install and launching R packages

The code chunk below uses p_load() of pacman package to check if FunnelPlotR, plotly, knitr and tidyverse packages are installed in the computer. If they are, then they will be launched into R.

pacman::p_load(tidyverse, FunnelPlotR, plotly, knitr)

covid19 <- read_csv("data/COVID-19_DKI_Jakarta.csv", show_col_types = FALSE) %>%
  mutate_if(is.character, as.factor)

FunnelPlotR

Basic Plot

funnel_plot(
  numerator = covid19$Positive,
  denominator = covid19$Death,
  group = covid19$`Sub-district`
)

A funnel plot object with 267 points of which 0 are outliers. 
Plot is adjusted for overdispersion.

Makeover 1

funnel_plot(
  numerator = covid19$Death,
  denominator = covid19$Positive,
  group = covid19$`Sub-district`,
  data_type = "PR",     #<<
  xrange = c(0, 6500),  #<<
  yrange = c(0, 0.05)   #<<
)

Warning: The `xrange` argument deprecated; please use the `x_range` argument
instead.  For more options, see the help: `?funnel_plot`

Warning: The `yrange` argument deprecated; please use the `y_range` argument
instead.  For more options, see the help: `?funnel_plot`

A funnel plot object with 267 points of which 7 are outliers. 
Plot is adjusted for overdispersion.

Makeover 2

funnel_plot(
  numerator = covid19$Death,
  denominator = covid19$Positive,
  group = covid19$`Sub-district`,
  data_type = "PR",   
  xrange = c(0, 6500),  
  yrange = c(0, 0.05),
  label = NA,
  title = "Cumulative COVID-19 Fatality Rate by Cumulative Total Number of COVID-19 Positive Cases", #<<           
  x_label = "Cumulative COVID-19 Positive Cases", #<<
  y_label = "Cumulative Fatality Rate"  #<<
)

Warning: The `xrange` argument deprecated; please use the `x_range` argument
instead.  For more options, see the help: `?funnel_plot`

Warning: The `yrange` argument deprecated; please use the `y_range` argument
instead.  For more options, see the help: `?funnel_plot`

A funnel plot object with 267 points of which 7 are outliers. 
Plot is adjusted for overdispersion.

Funnel Plot using ggplot2

Computing Derived Fields

df <- covid19 %>%
  mutate(rate = Death / Positive) %>%
  mutate(rate.se = sqrt((rate*(1-rate)) / (Positive))) %>%
  filter(rate > 0)

fit.mean <- weighted.mean(df$rate, 1/df$rate.se^2)

Computing Confidence Intervals

number.seq <- seq(1, max(df$Positive), 1)
number.ll95 <- fit.mean - 1.96 * sqrt((fit.mean*(1-fit.mean)) / (number.seq)) 
number.ul95 <- fit.mean + 1.96 * sqrt((fit.mean*(1-fit.mean)) / (number.seq)) 
number.ll999 <- fit.mean - 3.29 * sqrt((fit.mean*(1-fit.mean)) / (number.seq)) 
number.ul999 <- fit.mean + 3.29 * sqrt((fit.mean*(1-fit.mean)) / (number.seq)) 
dfCI <- data.frame(number.ll95, number.ul95, number.ll999, 
                   number.ul999, number.seq, fit.mean)

Static Funnel Plot

p <- ggplot(df, aes(x = Positive, y = rate)) +
  geom_point(aes(label=`Sub-district`), 
             alpha=0.4) +
  geom_line(data = dfCI, 
            aes(x = number.seq, 
                y = number.ll95), 
            size = 0.4, 
            colour = "grey40", 
            linetype = "dashed") +
  geom_line(data = dfCI, 
            aes(x = number.seq, 
                y = number.ul95), 
            size = 0.4, 
            colour = "grey40", 
            linetype = "dashed") +
  geom_line(data = dfCI, 
            aes(x = number.seq, 
                y = number.ll999), 
            size = 0.4, 
            colour = "grey40") +
  geom_line(data = dfCI, 
            aes(x = number.seq, 
                y = number.ul999), 
            size = 0.4, 
            colour = "grey40") +
  geom_hline(data = dfCI, 
             aes(yintercept = fit.mean), 
             size = 0.4, 
             colour = "grey40") +
  coord_cartesian(ylim=c(0,0.05)) +
  annotate("text", x = 1, y = -0.13, label = "95%", size = 3, colour = "grey40") + 
  annotate("text", x = 4.5, y = -0.18, label = "99%", size = 3, colour = "grey40") + 
  ggtitle("Cumulative Fatality Rate by Cumulative Number of COVID-19 Cases") +
  xlab("Cumulative Number of COVID-19 Cases") + 
  ylab("Cumulative Fatality Rate") +
  theme_light() +
  theme(plot.title = element_text(size=12),
        legend.position = c(0.91,0.85), 
        legend.title = element_text(size=7),
        legend.text = element_text(size=7),
        legend.background = element_rect(colour = "grey60", linetype = "dotted"),
        legend.key.height = unit(0.3, "cm"))

Warning in geom_point(aes(label = `Sub-district`), alpha = 0.4): Ignoring
unknown aesthetics: label

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Interactive Funnel Plot

fp_ggplotly <- ggplotly(p,
  tooltip = c("label", 
              "x", 
              "y"))
fp_ggplotly