Connor Rothschild

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Texas Vaccination Rates (How to Use Rayshader)

July 24, 2019

A brief exploration of Texas vaccination rates among kindergartners. Also an attempt to use rayshader for the first time.

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("2018-2019 School Vaccination Coverage Levels - Kindergarten (XLS) .xlsx", skip = 2)

kable(head(tx_vac))

Facility Number	School Type	Facility Name	Facility Address	County	DTP/DTaP/DT/Td	Hepatitis A	Hepatitis B	MMR	Polio	Varicella
9057816000	Public ISD	A W Brown Leadership Academy	5701 RED BIRD CTR DR, DALLAS, TX, 75237	Dallas	0.8317308	0.9086538	0.9471154	0.8509615	0.8413462	0.8509615
9057829000	Public ISD	A+ Academy	8225 BRUTON RD, DALLAS, TX, 75217	Dallas	1.0000000	1.0000000	1.0000000	0.9909091	1.0000000	1.0000000
9109901000	Public ISD	Abbott ISD	P O BOX 226, ABBOTT, TX, 76621	Hill	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000
7101130101	Private School	Abercrombie Academy	17102 Theiss Mail Road, Spring, TX, 77379	Harris	1.0000000	1.0000000	1.0000000	0.7500000	1.0000000	0.7500000
9095901000	Public ISD	Abernathy ISD	505 7TH ST, ABERNATHY, TX, 79311	Hale	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000
7101220001	Private School	Abiding Word Lutheran School	17123 Red Oak Drive, Houston, TX, 77090	Harris	0.7692308	0.7692308	0.7692308	0.7692308	0.6923077	0.7692308

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))

subregion	avgvac
anderson	0.9676797
andrews	0.9715335
angelina	0.9693150
aransas	0.9735294
archer	0.9915167
armstrong	0.9677419

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:

center

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)

## Error: package or namespace load failed for 'rayshader' in dyn.load(file, DLLpath = DLLpath, ...):
##  unable to load shared object '/usr/local/lib/R/3.6/site-library/igraph/libs/igraph.so':
##   dlopen(/usr/local/lib/R/3.6/site-library/igraph/libs/igraph.so, 6): Library not loaded: /usr/local/opt/openblas/lib/libopenblasp-r0.3.6.dylib
##   Referenced from: /usr/local/lib/R/3.6/site-library/igraph/libs/igraph.so
##   Reason: image not found

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)

You can see the output here:

rayshader