Quiz 2 Correction

What is the difference between the average age of death due to breast cancer for women within each of the following races WHITE , BLACK OR AFRICAN AMERICAN, ASIAN, and AMERICAN INDIAN OR ALASKA NATIVE?

Express this difference in years (or fraction of a year) and the resultant tibble should be sorted into ascending order by these average ages.

# Load the data and packages
library(tidyverse)

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.2     v purrr   0.3.4
v tibble  3.0.1     v dplyr   1.0.0
v tidyr   1.1.0     v stringr 1.4.0
v readr   1.3.1     v forcats 0.5.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

load("/Users/Aki/Desktop/small_brca.Rdata")

small_brca %>% 
  select(participant, gender, race, age_at_diagnosis, death_days_to) %>%
  filter(gender == "FEMALE" &
           # Select for samples from dead patients
           death_days_to != "[Not Applicable]" & 
           # Remove outliers
           race != "[Not Evaluated]" &  
           race != "[Not Available]") %>%
  # Filter by unique patients
  distinct(participant, .keep_all = TRUE) %>%
  # Add new column with age of death
  # The floor function rounds down. You don't need to do this
  mutate(age_of_death = as.numeric(age_at_diagnosis) + 
           floor(as.numeric(death_days_to)/365)) %>%
  # Group by race and summarise for mean
  group_by(race) %>%
  summarise(mean.age.of.death = mean(age_of_death), .groups = 'drop') %>%
  # Sorted into ascending order by mean.age.of.death
  arrange(mean.age.of.death)

Notice how AMERICAN INDIAN OR ALAKSA NATIVE is no longer in the result. This is because there was only one patient in that category and she is alive (death_days_to == “[Not Applicable]”), therefore, she was filtered out.

( which(small_brca$race == "AMERICAN INDIAN OR ALASKA NATIVE") )

[1] 660

c(small_brca[660, ]$vital_status, small_brca[660, ]$death_days_to)

[1] "Alive"            "[Not Applicable]"