In vjcitn/YESCDS: Cancer data science activities for CZI YES for CURE collaboration

suppressMessages({
 suppressPackageStartupMessages({
  library(YESCDS)
library(tibble)
library(dplyr)
library(plotly)
library(ggplot2)
library(ggbeeswarm)
library(DT)
data(woncan_meta)
data(woncan)
library(sf)
littab = woncan |> select(MSA, `Cancer Sites`, Age.Adjusted.Rate) |> as.data.frame()
  })
 })

Basic geographic data about US counties

The coordinates of central locations in US counties are provided in us_county_geo.

data(us_county_geo)
us_county_geo |> select(state, county, geometry) |> head()

Coordinates for metropolitan statistical areas are provided by "statcrunch":

data(statcrunch_msa)
head(statcrunch_msa)

This geographic data has already been used to enhance the CDC incidence data in woncan:

data(woncan)
woncan |> group_by(MSA) |> 
    summarize(lat=head(lat)[1], lng=head(lng)[1]) |> head()

Exercise

B.2.1 Create a new notebook cell and run YESCDS::table_woncan("Prostate")

B.2.2 Use this table to find the latitude and longitude of Boston.

Answers

B.2.1

B.2.2

An interactive map of the US with cancer rates

After combining cancer rate data for a collection of cancer types and metropolitan statistical areas, we can produce a map showing variation in cancer incidence over the United States. Here is the example for stomach cancer:

cancer_map_usa(site="Stomach")

Exercise

B.2.3 Create a new notebook cell and run cancer_map_usa(site="Prostate", scaling=0.05)

B.2.4 Can you identify the area with the highest incidence of prostate cancer?

Answers

B.2.3

B.2.4

A data graphic

Finally, to get a different view of variation in cancer rates across the United States, run a cell with the following command. Geographic location is lost, but the range of variation, and details of variation can be seen very clearly in these displays.

browseURL("https://vjcitn.shinyapps.io/ratevariation")

Exercise

B.2.5 Change the body site to "Pancreas" (remove "Brain") and find, using the histogram tab, the areas with highest and lowest age-adjusted rates of pancreatic cancer.