d should be allowed to equal p.

[nspyrison]

do.pca() still doesn't allow d to be equal to p which is fully valid. It currently silently drops a dimension.

dat <- mtcars[, 1:2]
Rdimtools::do.pca(X = as.matrix(dat), ndim = 2)
#> $Y
#>             [,1]
#>  [1,] -18.831637
#>  [2,] -18.831637
#>  [3,] -21.074684
#>  [4,] -19.218921
#>  [5,] -16.104483
#>  [6,] -16.023824
#>  [7,] -11.844353
#>  [8,] -22.623822
#>  [9,] -21.074684
#> [10,] -17.088856
#> [11,] -15.733360
#> [12,] -13.877597
#> [13,] -14.748987
#> [14,] -12.715744
#> [15,]  -8.068329
#> [16,]  -8.068329
#> [17,] -12.231638
#> [18,] -30.369513
#> [19,] -28.433090
#> [20,] -31.821830
#> [21,] -19.816009
#> [22,] -13.006207
#> [23,] -12.715744
#> [24,] -10.876142
#> [25,] -16.588589
#> [26,] -25.431635
#> [27,] -24.172960
#> [28,] -28.433090
#> [29,] -13.296670
#> [30,] -17.572962
#> [31,] -12.522101
#> [32,] -19.719188
#> 
#> $vars
#> [1] 38.69375
#> 
#> $projection
#>            [,1]
#> [1,] -0.9682113
#> [2,]  0.2501336
#> 
#> $algorithm
#> [1] "linear:PCA"
#> 
#> attr(,"class")
#> [1] "Rdimtools"

^{Created on 2023-03-20 with reprex v2.0.2}

[kisungyou]

@nspyrison I agree that this ninja operation can be an issue. I'm currently working on rewriting of the package whenever available (job market is just over) and will probably put a warning/message popping up for the user. However, d=p is just rotation by PCs and I am wondering whether it would be worth to allow this operation. I would appreciate your opinion as I want to be as much consistent as possible across all functionalities offered in this package.

[nspyrison]

Hi @kisungyou, thank you for your development work. Rotations are a valid and important aspect of exploring dimensions. IMHO d=p absolutely should be facilitated wherever possible.

I love the idea of your package, but I have had to roll back to prcomp and MASS::lda on more than one occasion because Rdimtools was developed with dim reduction in mind. The more general and extensible you make you can make the Rdimtools allow others to use and build on top of it, rather than being forced to seek the original implementations.

HTH