Texas Vaccination Rates (How to Use Rayshader)

Load Packages

library(readxl)
library(tidyverse)
library(stringr)
library(dplyr)
library(ggplot2)
library(ggmap)
library(maps)
library(mapdata)
library(scales)
library(tpltheme)
library(knitr)
conflicted::conflict_prefer("filter", "dplyr")

set_tpl_theme(font = "lato")

Read in Data

tx_vac <- read_excel("data/2018-2019 School Vaccination Coverage Levels - Kindergarten (XLS) .xlsx", skip = 2)

kable(head(tx_vac))

The data contains information on six different vaccines split up by school. The set also contains information on the county of each school, allowing us to aggregate on the county level. By finding the average of the six vaccines listed in this dataset, we can see average vaccination rate by county:

grouped <- tx_vac %>% 
  mutate(avgvac = (`DTP/DTaP/DT/Td`+`Hepatitis A`+`Hepatitis B`+MMR+Polio+Varicella)/6) %>%
  group_by(County) %>%
  summarize(avgvac = mean(avgvac, na.rm = TRUE)) %>%
  mutate(County = tolower(County)) %>%
  # rename to subregion so that we can later join with ggplot map data
  rename("subregion" = County) %>%
  filter(subregion != "king")

kable(head(grouped))

Next, we read in the county-level data from ggplot2 and merge it with our vaccination data:

counties <- map_data("county")
tx_county <- subset(counties, region == "texas")
merged <- left_join(tx_county, grouped, by = "subregion")

Plot

Construct the plot using geom_polygon(), and pay special attention to theme attributes (axes, panels, etc.).

Unfortunately, theme_nothing() led to some conflicts with rayshader, so I essentially recreated it using theme() attributes.

tx <- ggplot(data = merged, mapping = aes(x = long, y = lat, group = group, fill = avgvac*100)) +
  coord_fixed(1.3) +
  geom_polygon(color = "black") +
  labs(fill = "Vaccination Rate") +
  #theme_nothing(legend = TRUE) +
  theme(legend.title = element_text(),
        #legend.key.width = unit(.1, "in"),
        panel.border = element_blank(), panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), axis.line = element_blank(), 
        axis.text.x = element_blank(), axis.text.y = element_blank(),
        axis.ticks = element_blank(),
        panel.background = element_rect(fill = "white"),
        text = element_text(family = "Lato"),
        legend.position = "bottom") +
   labs(x = element_blank(),
        y = element_blank(),
        title = "Texas Vaccination Rate by County",
        subtitle = "Among Kindergartners") + 
  tpltheme::scale_fill_continuous()

Here’s what the plot looks like before animation:

Rayshader

Load in rayshader and rgl. I’m not sure if rgl is necessary for all R users, but I ran into a few errors on my system (Mac) prior to its installation.

#devtools::install_github("tylermorganwall/rayshader")
library(rgl)
options(rgl.useNULL = FALSE)
library(rayshader)

Lastly, create the plot_gg() object by following the comprehensive documentation on Wall’s README.

par(mfrow = c(1,1))
rayshader::plot_gg(tx, width = 5, raytrace = TRUE, multicore = TRUE, height = 5, scale = 50)

# create custom rotation parameters here
phivechalf = 30 + 60 * 1/(1 + exp(seq(-7, 20, length.out = 180)/2))
phivecfull = c(phivechalf, rev(phivechalf))
thetavec = -90 + 60 * sin(seq(0,359,length.out = 360) * pi/180)
zoomvec = 0.45 + 0.2 * 1/(1 + exp(seq(-5, 20, length.out = 180)))
zoomvecfull = c(zoomvec, rev(zoomvec))

render_movie(filename = "outputs/tx_vac_vid", type = "custom", 
             frames = 360,  phi = phivecfull, zoom = zoomvecfull, theta = thetavec)