SVI and health outcome • findSVI

Designed to represent the relative resilience of communities within an area, SVI not only provides valuable information for local officials/policymakers in planning and managing public health emergencies, but also offers an important neighborhood metric to facilitate public health research, such as the correlation between health outcome and SVI (and the socioeconomic/demographic factors involved) of a certain area.

For example, to investigate the possible correlation between the COVID-19-related deaths and SVI in Philadelphia at the ZCTA level, we could use findSVI to get ZCTA-level SVI for Philadelphia (with geometry) and join the result with ZCTA-level COVID-19 data for visualization and correlation analysis.

As usual, we start with loading all the packages needed.

library(findSVI)
library(dplyr)
library(sf)
library(tidyr)
library(tmap)
library(ggplot2)

ZCTA-level SVI in Philadelphia for 2020

For retrieving census data with geometry, we’ll use get_census_data() and get_svi() to obtain SVI. We’ll keep the GEOID(ZCTA) and SVI-related columns in the resulting SVI table.

phl_zcta_data_geo_2020 <- get_census_data(
  2020,
  geography = "zcta",
  state = "PA",
  county = "Philadelphia",
  geometry = TRUE
)

phl_zcta_svi_geo_2020 <- get_svi(2020,
  data = phl_zcta_data_geo_2020) %>%
  select(GEOID, contains("RPL_theme"))

phl_zcta_svi_geo_2020 %>% glimpse()

#> Rows: 48
#> Columns: 7
#> $ GEOID      <chr> "19102", "19103", "19104", "19106", "19107", "19109", "1911…
#> $ RPL_theme1 <dbl> 0.0444, 0.0222, 0.6889, 0.0000, 0.3333, NA, 0.5778, NA, 0.1…
#> $ RPL_theme2 <dbl> 0.0222, 0.2222, 0.2000, 0.1111, 0.0667, NA, 0.8667, NA, 0.4…
#> $ RPL_theme3 <dbl> 0.0889, 0.1778, 0.5556, 0.0444, 0.4000, NA, 0.5111, NA, 0.1…
#> $ RPL_theme4 <dbl> 0.9556, 0.9333, 0.9778, 0.7111, 1.0000, NA, 0.5778, NA, 0.1…
#> $ RPL_themes <dbl> 0.1778, 0.2667, 0.6889, 0.0444, 0.3778, NA, 0.7111, NA, 0.2…
#> $ geometry   <MULTIPOLYGON [°]> MULTIPOLYGON (((-75.16854 3..., MULTIPOLYGON (…

ZCTA-level COVID-19 data in Philadelphia

Disease-related data at the ZCTA level is usually not easily accessible for privacy reasons. Here, we’ll use data from the COVID-19 Health Inequities in Cities Dashboard, a great resource released by Drexel University’s Urban Health Collaborative and the Big Cities Health Coalition (BCHC). In addition to data available for download, the dashboard provides informative visualizations of COVID-19 related outcomes and inequities over time and across BCHC cities.

After downloading the raw data, we can select Philadelphia city and the variables of interest (hospitalization per 100k).

#source:https://github.com/Drexel-UHC/covid_inequities_project
#bchc_raw <- read_csv("../../byZCTA_bchc.csv")

phl_hosp <- bchc_raw %>%
  filter(city == "Philadelphia") %>%
  mutate(GEOID = paste(zcta), .after = zcta) %>%
  select(GEOID, hosp_per_100k)

glimpse(phl_hosp)

#> Rows: 46
#> Columns: 2
#> $ GEOID         <chr> "19102", "19103", "19104", "19106", "19107", "19111", "1…
#> $ hosp_per_100k <dbl> 194.288, 846.618, 1280.807, 405.019, 1555.831, 1133.411,…

Joining data for visualzation

Once we have the ZCTA-level SVI and COVID-19 data ready, we can join them together by GEOID(ZCTA), keeping the spatial information.

phl_svi_covid <- phl_hosp %>%
  left_join(phl_zcta_svi_geo_2020, by = "GEOID") %>%
  #although geometry sticky, after wrangling, class() become df
  st_as_sf(sf_column_name = "geometry")

phl_svi_covid %>% head(10)
#> Simple feature collection with 10 features and 7 fields
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -75.24074 ymin: 39.92578 xmax: -74.97371 ymax: 40.13799
#> Geodetic CRS:  NAD83
#> # A tibble: 10 × 8
#>    GEOID hosp_per_100k RPL_theme1 RPL_theme2 RPL_theme3 RPL_theme4 RPL_themes
#>    <chr>         <dbl>      <dbl>      <dbl>      <dbl>      <dbl>      <dbl>
#>  1 19102          194.     0.0444     0.0222     0.0889      0.956     0.178 
#>  2 19103          847.     0.0222     0.222      0.178       0.933     0.267 
#>  3 19104         1281.     0.689      0.2        0.556       0.978     0.689 
#>  4 19106          405.     0          0.111      0.0444      0.711     0.0444
#>  5 19107         1556.     0.333      0.0667     0.4         1         0.378 
#>  6 19111         1133.     0.578      0.867      0.511       0.578     0.711 
#>  7 19114         1336.     0.178      0.422      0.156       0.111     0.2   
#>  8 19115         1502.     0.378      0.822      0.289       0.822     0.533 
#>  9 19116         1226.     0.4        0.733      0.244       0.622     0.489 
#> 10 19118         1038.     0.156      0.289      0.2         0.267     0.133 
#> # ℹ 1 more variable: geometry <MULTIPOLYGON [°]>

Maps

To visualize their spatial pattern directly, we can plot the SVI and COVID-19 data in Philadelphia neighborhoods (ZCTAs) directly on maps:


covid_hosp <- phl_svi_covid %>%
  select(GEOID, geometry, hosp_per_100k) %>%
  drop_na() %>% 
  tm_shape(projection = sf::st_crs(26915))+
  tm_polygons("hosp_per_100k",
    style = "quantile",
    title = "Hospitalizations/100k")+
  tm_layout(title = "COVID-19 Hospitalizations",
    title.size = 1,
    title.position = c("left", "TOP"),
    legend.position = c("RIGHT", "bottom"),
    legend.title.size = 0.9,
    legend.width = 2)

svi <- phl_svi_covid %>%
  select(GEOID, geometry, RPL_themes) %>%
  drop_na() %>%
  tm_shape(projection = sf::st_crs(26915))+
  tm_polygons("RPL_themes",
    style = "quantile",
    title = "Overall SVI (2020)",
    palette = "Blues")+
  tm_layout(title = "Social Vulnerability",
    title.size = 1,
    title.position = c("left", "TOP"),
    legend.position = c("RIGHT", "bottom"),
    legend.title.size = 0.9,
    legend.width = 2)

plots <- list(svi, covid_hosp)

current.mode <- tmap_mode("plot")
#> tmap mode set to plotting

#> tmap mode set to plotting

tmap_arrange(
  plots, 
  nrow = 1,
  width = c(0.5, 0.5)
  )

SVI and COVID-19 hospitalizations in Philadelphia Neighborhoods (ZCTAs). COVID-19 data are cumulative till 8/2022.

Correlation

To look at possible correlation between SVI and COVID-19 hospitalizations, we’ll use scatter plot to visualize their relationships:

phl_svi_covid %>%
  ggplot(aes(x = RPL_themes, y = hosp_per_100k)) +
  geom_point()+
  labs(
    title = "Social Vulnerability and COVID-19 Hospitalizations \nin Philadelphia Neighborhoods",
    caption = "COVID-19 data are cumulative till 8/2022", 
    x = "Overall SVI (2020)",
    y = "Hospitalizations per 100k") +
  theme_bw()+
  theme(
    text = element_text(size = 13),
    plot.title = element_text(size = 14, face = "bold"),
    axis.title = element_text(size = 12, face = "bold"),
    legend.title = element_text(size = 13),
    plot.caption = element_text(size = 9, color = "#4D4948")
  )

With a correlation coefficient of 0.7030584, overall SVI is shown to be strongly associated with COVID-19 hospitalizations in Philadelphia neighborhoods, where higher hospitalization rate is found in neighborhoods with higher social vulnerability.

This is consistent with the story on the COVID-19 Health Inequities in Cities Dashboard, where they found most socially vulnerable neighborhoods have 129.4% higher hospitalizations per 100k compared to the least socially vulnerable neighborhoods.

Reference

Diez Roux, A., Kolker, J., Barber, S., Bilal, U., Mullachery, P., Schnake-Mahl, A., McCulley, E., Vaidya, V., Ran, L., Rollins, H., Furukawa, A., Koh, C., Sharaf, A., Dureja, K. (2021). COVID-19 Health Inequities In Cities Dashboard. Drexel University: Urban Health Collaborative. http://www.covid-inequities.info/.