Comparing DRR and PCA

This is an example application to compare the accuracy and computational speed of DRR for different parameters to PCA.

Load libraries

library(DRR)
set.seed(123)

Read in data

data(iris)

in_data <- iris[, 1:4]

npoints <- nrow(in_data)
nvars <- ncol(in_data)
for (i in seq_len(nvars)) in_data[[i]] <- as.numeric(in_data[[i]])
my_data <- scale(in_data[sample(npoints), ], scale = FALSE)

Fit the dimensionality reductions.

t0 <- system.time(pca   <- prcomp(my_data, center = FALSE, scale. = FALSE))
t1 <- system.time(drr.1 <- drr(my_data, verbose = FALSE))
t2 <- system.time(drr.2 <- drr(my_data, fastkrr = 2, verbose = FALSE))
t3 <- system.time(drr.3 <- drr(my_data, fastkrr = 5, verbose = FALSE))
t4 <- system.time(drr.4 <- drr(my_data, fastkrr = 2, fastcv = TRUE,
                               verbose = FALSE))

Plot the data

Calculate RMSE

rmse <- matrix(NA_real_, nrow = 5, ncol = nvars,
               dimnames = list(c("pca", "drr.1", "drr.2", "drr.3", "drr.4"),
                               seq_len(nvars)))

for (i in seq_len(nvars)){
    pca_inv <-
        pca$x[, 1:i, drop = FALSE] %*%
        t(pca$rotation[, 1:i, drop = FALSE])
    rmse["pca",   i] <-
        sqrt( sum( (
            my_data - pca_inv
        ) ^ 2 ) )
    rmse["drr.1", i] <-
        sqrt( sum( (
            my_data - drr.1$inverse(drr.1$fitted.data[, 1:i, drop = FALSE])
        ) ^ 2 ) )
    rmse["drr.2", i] <-
        sqrt( sum( (
            my_data - drr.2$inverse(drr.2$fitted.data[, 1:i, drop = FALSE])
        ) ^ 2) )
    rmse["drr.3", i] <-
        sqrt( sum( (
            my_data - drr.3$inverse(drr.3$fitted.data[, 1:i, drop = FALSE])
        ) ^ 2) )
    rmse["drr.4", i] <-
        sqrt( sum( (
            my_data - drr.4$inverse(drr.4$fitted.data[, 1:i, drop = FALSE])
        ) ^ 2) )
}

The Results

More blocks for fastkrr speed up calculation, too are bad for accuracy.

RMSE

##              1        2        3            4
## pca   7.166770 3.899313 1.884524 6.673051e-15
## drr.1 5.602073 3.436881 1.709814 1.335532e-14
## drr.2 5.514719 3.211950 1.643146 1.340926e-14
## drr.3 5.726228 3.496065 1.724555 1.336149e-14
## drr.4 5.547636 2.889650 1.643971 1.410265e-14

Processing time

##       user.self sys.self elapsed
## pca       0.001    0.001   0.001
## drr.1    10.827    0.019  10.847
## drr.2     6.309    0.004   6.313
## drr.3    13.443    0.016  13.460
## drr.4    13.755    0.004  13.760