Tasting

Analysis of Prostate Data

prostate |> 
  mutate(aa = factor(aa, levels = c(0, 1),
                     labels = c("White", "African-American"))) |> 
  mutate(fam_hx = factor(fam_hx, levels = c(0, 1),
                         labels = c("No Family History", "Fhx of Prostate Cancer"))) ->
  prostate_factors

prostate_factors |> 
  select(age, p_vol, preop_psa, aa, fam_hx) |> 
  group_by(aa, fam_hx) |> 
  summarize(across(age:preop_psa, ~ mean(.x, na.rm = TRUE)))

## `summarise()` has grouped output by 'aa'. You can override using the `.groups`
## argument.

## # A tibble: 4 × 5
## # Groups:   aa [2]
##   aa               fam_hx                   age p_vol preop_psa
##   <fct>            <fct>                  <dbl> <dbl>     <dbl>
## 1 White            No Family History       61.8  56.9      8.06
## 2 White            Fhx of Prostate Cancer  59.5  57.3      7.22
## 3 African-American No Family History       60.7  54.3      9.90
## 4 African-American Fhx of Prostate Cancer  60.1  51.4      8.71

ggplot(prostate_factors) +
  aes(x = p_vol, y = preop_psa, colour = aa) +
  geom_point() +
  geom_smooth(method = "lm") +
  facet_grid(aa ~fam_hx) + 
  labs(x = "Prostate Volume", y = "Preoperative PSA",
       title = "Relationship Between Prostate Volume and Preop PSA, \nSubdivided by Family History and Race") +
  theme(legend.position = "bottom")

## `geom_smooth()` using formula = 'y ~ x'

## Warning: Removed 11 rows containing non-finite outside the scale range
## (`stat_smooth()`).

## Warning: Removed 11 rows containing missing values or values outside the scale range
## (`geom_point()`).

Statistical Testing

prostate_factors |> 
  t_test(formula = preop_psa ~aa,
         detailed = TRUE)

## # A tibble: 1 × 15
##   estimate estimate1 estimate2 .y.    group1 group2    n1    n2 statistic      p
## *    <dbl>     <dbl>     <dbl> <chr>  <chr>  <chr>  <int> <int>     <dbl>  <dbl>
## 1    -1.89      7.86      9.75 preop… White  Afric…   259    54     -1.96 0.0534
## # ℹ 5 more variables: df <dbl>, conf.low <dbl>, conf.high <dbl>, method <chr>,
## #   alternative <chr>