tidy.prcomp() returns incorrect result with method = "rotation"

[clauswilke]

When using tidy() on a prcomp object with method = "rotation" to extract the rotation matrix, the output that is returned is incorrect. The problem is that the PCs are numbered incorrectly. We would expect each variable in the original dataset to be paired exactly once with each PC. Instead, the first variable is paired multiple times with the first PC, the second variable is paired multiple times with the second PC, and so on. Reprex follows below.

library(broom)
library(dplyr)
library(tidyr)

iris_pca <- iris %>%
  select(-Species) %>%
  scale() %>%
  prcomp()

# output generated by tidy.prcomp()
tidy(iris_pca, matrix = "rotation")
#> # A tibble: 16 x 3
#>    column          PC   value
#>    <chr>        <dbl>   <dbl>
#>  1 Sepal.Length     1  0.521 
#>  2 Sepal.Width      2 -0.377 
#>  3 Petal.Length     3  0.720 
#>  4 Petal.Width      4  0.261 
#>  5 Sepal.Length     1 -0.269 
#>  6 Sepal.Width      2 -0.923 
#>  7 Petal.Length     3 -0.244 
#>  8 Petal.Width      4 -0.124 
#>  9 Sepal.Length     1  0.580 
#> 10 Sepal.Width      2 -0.0245
#> 11 Petal.Length     3 -0.142 
#> 12 Petal.Width      4 -0.801 
#> 13 Sepal.Length     1  0.565 
#> 14 Sepal.Width      2 -0.0669
#> 15 Petal.Length     3 -0.634 
#> 16 Petal.Width      4  0.524

# expected output would be something like this
iris_pca$rotation %>%
  as.data.frame() %>%
  mutate(column = row.names(.)) %>%
  pivot_longer(PC1:PC4) %>%
  arrange(name, column)
#> # A tibble: 16 x 3
#>    column       name    value
#>    <chr>        <chr>   <dbl>
#>  1 Petal.Length PC1    0.580 
#>  2 Petal.Width  PC1    0.565 
#>  3 Sepal.Length PC1    0.521 
#>  4 Sepal.Width  PC1   -0.269 
#>  5 Petal.Length PC2   -0.0245
#>  6 Petal.Width  PC2   -0.0669
#>  7 Sepal.Length PC2   -0.377 
#>  8 Sepal.Width  PC2   -0.923 
#>  9 Petal.Length PC3   -0.142 
#> 10 Petal.Width  PC3   -0.634 
#> 11 Sepal.Length PC3    0.720 
#> 12 Sepal.Width  PC3   -0.244 
#> 13 Petal.Length PC4   -0.801 
#> 14 Petal.Width  PC4    0.524 
#> 15 Sepal.Length PC4    0.261 
#> 16 Sepal.Width  PC4   -0.124

^{Created on 2020-09-03 by the reprex package (v0.3.0)}

[clauswilke]

I suspect a fix would be to write label = rep(labels, each = ncomp) here:

broom/R/stats-prcomp-tidiers.R

Line 126 in 5da04f6

label = rep(labels, times = ncomp),

Though that assumes a specific behavior of tidyr::pivot_longer() and may break in the future. A safer implementation would add the variable names to the data frame before pivoting, as shown in my reprex above.

[simonpcouch]

The thoroughness is much appreciated!

Related to #924 and #910. Closing in favor of #910.

[clauswilke]

Thanks! Will there be another broom release his fall? I'm hoping to use this feature in a class I'll be teaching next spring.

[simonpcouch]

I'm hoping to wrap up patches from 0.7.0 in the next week or two and then will move towards revdepchecks! I'm hesitant to give any explicit timeline, as I've only had one go through the broom release process, but a fall release is definitely the goal. :-)

[github-actions]

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