Healthy Cities GIS Assignment

Author

Lena

Load the libraries and set the working directory

options(repos = "https://cran.r-project.org")
install.packages("leaflet")
package 'leaflet' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\kwils\AppData\Local\Temp\RtmpmOYJfH\downloaded_packages
install.packages("sf")
package 'sf' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\kwils\AppData\Local\Temp\RtmpmOYJfH\downloaded_packages
library(tidyverse)
library(tidyr)
library(sf)
library(leaflet)
library(knitr)
library(dplyr)
library(plotly)
library(ggplot2)
setwd("C:/Users/kwils/OneDrive/Desktop/DATA 110")
cities500 <- read_csv("500CitiesLocalHealthIndicators.cdc.csv")

The GeoLocation variable has (lat, long) format

Split GeoLocation (lat, long) into two columns: lat and long

latlong <- tidyr::extract(cities500, GeoLocation, c('lat', 'long'), 
               regex = ',?\\s*\\((\\d+\\.\\d+).*(-?\\d+\\.\\d+)\\)')
head(latlong)
# A tibble: 6 × 25
   Year StateAbbr StateDesc  CityName  GeographicLevel DataSource Category      
  <dbl> <chr>     <chr>      <chr>     <chr>           <chr>      <chr>         
1  2017 CA        California Hawthorne Census Tract    BRFSS      Health Outcom…
2  2017 CA        California Hawthorne City            BRFSS      Unhealthy Beh…
3  2017 CA        California Hayward   City            BRFSS      Health Outcom…
4  2017 CA        California Hayward   City            BRFSS      Unhealthy Beh…
5  2017 CA        California Hemet     City            BRFSS      Prevention    
6  2017 CA        California Indio     Census Tract    BRFSS      Health Outcom…
# ℹ 18 more variables: UniqueID <chr>, Measure <chr>, Data_Value_Unit <chr>,
#   DataValueTypeID <chr>, Data_Value_Type <chr>, Data_Value <dbl>,
#   Low_Confidence_Limit <dbl>, High_Confidence_Limit <dbl>,
#   Data_Value_Footnote_Symbol <chr>, Data_Value_Footnote <chr>,
#   PopulationCount <dbl>, lat <chr>, long <chr>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>

Filter the dataset

Remove the StateDesc that includes the United Sates, select Prevention as the category (of interest), filter for only measuring crude prevalence and select only 2017.

latlong_clean <- latlong |>
  filter(StateDesc != "United States") |>
  filter(Category == "Prevention") |>
  filter(Data_Value_Type == "Crude prevalence") |>
  filter(Year == 2017)
head(latlong_clean)
# A tibble: 6 × 25
   Year StateAbbr StateDesc  CityName   GeographicLevel DataSource Category  
  <dbl> <chr>     <chr>      <chr>      <chr>           <chr>      <chr>     
1  2017 AL        Alabama    Montgomery City            BRFSS      Prevention
2  2017 CA        California Concord    City            BRFSS      Prevention
3  2017 CA        California Concord    City            BRFSS      Prevention
4  2017 CA        California Fontana    City            BRFSS      Prevention
5  2017 CA        California Richmond   Census Tract    BRFSS      Prevention
6  2017 FL        Florida    Davie      Census Tract    BRFSS      Prevention
# ℹ 18 more variables: UniqueID <chr>, Measure <chr>, Data_Value_Unit <chr>,
#   DataValueTypeID <chr>, Data_Value_Type <chr>, Data_Value <dbl>,
#   Low_Confidence_Limit <dbl>, High_Confidence_Limit <dbl>,
#   Data_Value_Footnote_Symbol <chr>, Data_Value_Footnote <chr>,
#   PopulationCount <dbl>, lat <chr>, long <chr>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>

What variables are included? (can any of them be removed?)

names(latlong_clean)
 [1] "Year"                       "StateAbbr"                 
 [3] "StateDesc"                  "CityName"                  
 [5] "GeographicLevel"            "DataSource"                
 [7] "Category"                   "UniqueID"                  
 [9] "Measure"                    "Data_Value_Unit"           
[11] "DataValueTypeID"            "Data_Value_Type"           
[13] "Data_Value"                 "Low_Confidence_Limit"      
[15] "High_Confidence_Limit"      "Data_Value_Footnote_Symbol"
[17] "Data_Value_Footnote"        "PopulationCount"           
[19] "lat"                        "long"                      
[21] "CategoryID"                 "MeasureId"                 
[23] "CityFIPS"                   "TractFIPS"                 
[25] "Short_Question_Text"       

Remove the variables that will not be used in the assignment

prevention <- latlong_clean |>
  select(-DataSource,-Data_Value_Unit, -DataValueTypeID, -Low_Confidence_Limit, -High_Confidence_Limit, -Data_Value_Footnote_Symbol, -Data_Value_Footnote)
head(prevention)
# A tibble: 6 × 18
   Year StateAbbr StateDesc  CityName  GeographicLevel Category UniqueID Measure
  <dbl> <chr>     <chr>      <chr>     <chr>           <chr>    <chr>    <chr>  
1  2017 AL        Alabama    Montgome… City            Prevent… 151000   Choles…
2  2017 CA        California Concord   City            Prevent… 616000   Visits…
3  2017 CA        California Concord   City            Prevent… 616000   Choles…
4  2017 CA        California Fontana   City            Prevent… 624680   Visits…
5  2017 CA        California Richmond  Census Tract    Prevent… 0660620… Choles…
6  2017 FL        Florida    Davie     Census Tract    Prevent… 1216475… Choles…
# ℹ 10 more variables: Data_Value_Type <chr>, Data_Value <dbl>,
#   PopulationCount <dbl>, lat <chr>, long <chr>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>

The new dataset “Prevention” is a manageable dataset now.

latlong <- cities500|>
  mutate(GeoLocation = str_replace_all(GeoLocation, "[()]", ""))|>
  separate(GeoLocation, into = c("lat", "long"), sep = ",", convert = TRUE)
head(latlong)
# A tibble: 6 × 25
   Year StateAbbr StateDesc  CityName  GeographicLevel DataSource Category      
  <dbl> <chr>     <chr>      <chr>     <chr>           <chr>      <chr>         
1  2017 CA        California Hawthorne Census Tract    BRFSS      Health Outcom…
2  2017 CA        California Hawthorne City            BRFSS      Unhealthy Beh…
3  2017 CA        California Hayward   City            BRFSS      Health Outcom…
4  2017 CA        California Hayward   City            BRFSS      Unhealthy Beh…
5  2017 CA        California Hemet     City            BRFSS      Prevention    
6  2017 CA        California Indio     Census Tract    BRFSS      Health Outcom…
# ℹ 18 more variables: UniqueID <chr>, Measure <chr>, Data_Value_Unit <chr>,
#   DataValueTypeID <chr>, Data_Value_Type <chr>, Data_Value <dbl>,
#   Low_Confidence_Limit <dbl>, High_Confidence_Limit <dbl>,
#   Data_Value_Footnote_Symbol <chr>, Data_Value_Footnote <chr>,
#   PopulationCount <dbl>, lat <dbl>, long <dbl>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>

For your assignment, work with the cleaned “Prevention” dataset

1. Once you run the above code, filter this dataset one more time for any particular subset.

Filter chunk here

#extracting data related to Montgomery, Alabama
ALA_data <- prevention |>
  filter(!is.na(Data_Value), StateDesc == "Alabama", CityName == "Montgomery")
head(ALA_data)
# A tibble: 6 × 18
   Year StateAbbr StateDesc CityName   GeographicLevel Category UniqueID Measure
  <dbl> <chr>     <chr>     <chr>      <chr>           <chr>    <chr>    <chr>  
1  2017 AL        Alabama   Montgomery City            Prevent… 151000   Choles…
2  2017 AL        Alabama   Montgomery Census Tract    Prevent… 0151000… Taking…
3  2017 AL        Alabama   Montgomery Census Tract    Prevent… 0151000… Choles…
4  2017 AL        Alabama   Montgomery Census Tract    Prevent… 0151000… Visits…
5  2017 AL        Alabama   Montgomery Census Tract    Prevent… 0151000… Visits…
6  2017 AL        Alabama   Montgomery City            Prevent… 151000   Visits…
# ℹ 10 more variables: Data_Value_Type <chr>, Data_Value <dbl>,
#   PopulationCount <dbl>, lat <chr>, long <chr>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>

2. Based on the GIS tutorial (Japan earthquakes), create one plot about something in your subsetted dataset.

First plot chunk here

#scatter plot

ggplot(ALA_data, aes(x = MeasureId, y = Data_Value, color = MeasureId)) +
  geom_point() +
  geom_jitter() +
  labs(title = "Preventive Measures in Montgomery, Alabama ",
       x = "Measure ID",
       y = "Data Value",
       color = "Measure",
       caption = "Data from 2017, Source: CDC") +
  scale_color_brewer(palette = "Spectral") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))

3. Now create a map of your subsetted dataset.

First map chunk here

#

AL_data <- prevention |>
  filter(!is.na(Data_Value), StateDesc == "Alabama", MeasureId == "BPMED")
head(AL_data)
# A tibble: 6 × 18
   Year StateAbbr StateDesc CityName   GeographicLevel Category UniqueID Measure
  <dbl> <chr>     <chr>     <chr>      <chr>           <chr>    <chr>    <chr>  
1  2017 AL        Alabama   Mobile     Census Tract    Prevent… 0150000… Taking…
2  2017 AL        Alabama   Montgomery Census Tract    Prevent… 0151000… Taking…
3  2017 AL        Alabama   Mobile     Census Tract    Prevent… 0150000… Taking…
4  2017 AL        Alabama   Huntsville Census Tract    Prevent… 0137000… Taking…
5  2017 AL        Alabama   Mobile     Census Tract    Prevent… 0150000… Taking…
6  2017 AL        Alabama   Birmingham Census Tract    Prevent… 0107000… Taking…
# ℹ 10 more variables: Data_Value_Type <chr>, Data_Value <dbl>,
#   PopulationCount <dbl>, lat <chr>, long <chr>, CategoryID <chr>,
#   MeasureId <chr>, CityFIPS <dbl>, TractFIPS <dbl>, Short_Question_Text <chr>
AL_data$lat <- as.numeric(AL_data$lat)
AL_data$long <- as.numeric(AL_data$long)
AL_lat <- 32.8067
AL_lon <- -86.7911
leaflet(data = AL_data) |>
  addTiles() |>
  addCircles(lng = ~long, lat = ~lat) |>
  setView(lng = AL_lon, lat = AL_lat, zoom = 6)

4. Refine your map to include a mousover tooltip

AL_popup <- paste0(
      "<b>City: </b>", AL_data$CityName, "<br>",
      "<b>Population: </b>", AL_data$PopulationCount, "<br>",
      "<b>Taking BP Meds: </b>", AL_data$Data_Value, "%")
leaflet(data = AL_data) |>
  addTiles() |>
  addCircles(lng = ~long, lat = ~lat, popup = AL_popup) |>
  setView(lng = AL_lon, lat = AL_lat, zoom = 6)

5. Write a paragraph


The initial scatterplot provides an in-depth look at Montgomery, Alabama’s efforts in preventive healthcare. It focuses on key factors like access to healthcare services, blood pressure medication adherence, regular checkups, and cholesterol screening. This visual representation helps to understand how these health measures are distributed throughout the city.

Following this analysis, we have a map showcasing Montgomery, Alabama. It not only outlines the city’s boundaries but also provides important demographic data. This includes the city’s population and the percentage of people taking blood pressure medication. Together, these visuals give us a clearer picture of Montgomery’s health landscape.