calvaria: Data on calvaria growth in rat skulls

In GeodRegr: Geodesic Regression

Description

Vilmann data for growth in rat calvariae, that is, upper skulls, for 21 rats. For each rat, the shape of the calavaria was measured at 8 different ages (7, 14, 21, 30, 40, 60, 90, and 150 days), for a total of 168 data points. The boundaries of the midsagittal sections of the rats' calvariae are each marked with 8 landmarks. The data points have been translated and scaled in order to make them preshapes.

Usage

data(calvaria)

Format

A named list containing x a vector containing the ages y a matrix where each column is a preshape. The 23rd, 101st, 104th, and 160th entries are corrupted)

Details

There are 4 corrupted data points: those corresponding to day 90 for the 3rd rat, day 40 and 150 for the 13th rat, and day 150 for the 20th rat (the 23rd, 101st, 104th, and 160th entries); one of the landmarks for each of these measurements has been entered as (9999, 9999) (before translation/scaling).

Source

Vilmann's rat data set from pp. 408-414 of Bookstein. Original data available at https://www.sbmorphometrics.org/data/Book-VilmannRat.txt.

References

Bookstein, F. L. (1991). Morphometric Tools for Landmark Data: Geometry and Biology. Cambridge Univ, 408-414.

Hinkle, J., Muralidharan, P., Fletcher, P. T., Joshi, S. (2012). Polynomial Regression on Riemannian Manifolds. European Conference on Computer Vision, 1-14.

Examples

# we will test the robustness of each estimator by comparing their
# performance on the original (corrupted) data set to that of the L_2
# estimator on the uncorrupted data set (with the 4 problematic data points
# removed).

data(calvaria)

manifold <- 'kendall'

contam_x_data <- calvaria$x
contam_mean_x <- mean(contam_x_data)
contam_x_data <- contam_x_data - contam_mean_x # center x data
uncontam_x_data <- calvaria$x[ -c(23, 101, 104, 160)]
uncontam_mean_x <- mean(uncontam_x_data)
uncontam_x_data <- uncontam_x_data - uncontam_mean_x # center x data

contam_y_data <- calvaria$y
uncontam_y_data <- calvaria$y[, -c(23, 101, 104, 160)] # remove corrupted
    # columns

landmarks <- dim(contam_y_data)[1]
dimension <- 2 * landmarks - 4

# we ignore Huber's estimator as the L_1 estimator already has an
# (approximate) efficiency above 95% in 12 dimensions; see documentation for
# the are and are_nr functions

tol <- 1e-5
uncontam_l2 <- geo_reg(manifold, uncontam_x_data, uncontam_y_data,
    'l2', p_tol = tol, V_tol = tol)
contam_l2 <- geo_reg(manifold, contam_x_data, contam_y_data,
    'l2', p_tol = tol, V_tol = tol)
contam_l1 <- geo_reg(manifold, contam_x_data, contam_y_data,
    'l1', p_tol = tol, V_tol = tol)
contam_tukey <- geo_reg(manifold, contam_x_data, contam_y_data,
    'tukey', are_nr('tukey', dimension, 10, 0.99), p_tol = tol, V_tol = tol)

geodesics <- vector('list')
geodesics[[1]] <- uncontam_l2
geodesics[[2]] <- contam_l2
geodesics[[3]] <- contam_l1
geodesics[[4]] <- contam_tukey

loss(manifold, geodesics[[1]]$p, geodesics[[1]]$V, uncontam_x_data,
    uncontam_y_data, 'l2')
loss(manifold, geodesics[[2]]$p, geodesics[[2]]$V, contam_x_data,
    contam_y_data, 'l2')
loss(manifold, geodesics[[3]]$p, geodesics[[3]]$V, contam_x_data,
    contam_y_data, 'l1')
loss(manifold, geodesics[[4]]$p, geodesics[[4]]$V, contam_x_data,
    contam_y_data, 'tukey', are_nr('tukey', dimension, 10, 0.99))

# visualization of each geodesic

oldpar <- par(mfrow = c(1, 4))

days <- c(7, 14, 21, 30, 40, 60, 90, 150)
pal <- colorRampPalette(c("blue", "red"))(length(days))

# each predicted geodesic will be represented as a sequence of the predicted
# shapes at each of the above ages, the blue contour will show the predicted
# shape on day 7 and the red contour the predicted shape on day 150

contour <- vector('list')

for (i in 1:length(days)) {
  contour[[i]] <- exp_map(manifold, geodesics[[1]]$p, (days[i] -
      uncontam_mean_x) * geodesics[[1]]$V)
  contour[[i]] <- c(contour[[i]], contour[[i]][1])
}
plot(Re(contour[[length(days)]]), Im(contour[[length(days)]]), type = 'n',
    xaxt = 'n', yaxt = 'n', ann = FALSE, asp = 1)
 for (i in 1:length(days)) {
   lines(Re(contour[[i]]), Im(contour[[i]]), col = pal[i])
}
for (j in 2:4) {
  for (i in 1:length(days)) {
    contour[[i]] <- exp_map(manifold, geodesics[[j]]$p, (days[i] -
        contam_mean_x) * geodesics[[j]]$V)
    contour[[i]] <- c(contour[[i]], contour[[i]][1])
  }
  plot(Re(contour[[length(days)]]), Im(contour[[length(days)]]), type = 'n',
      xaxt = 'n', yaxt = 'n', ann = FALSE, asp = 1)
  for (i in 1:length(days)) {
    lines(Re(contour[[i]]), Im(contour[[i]]), col = pal[i])
  }
}
# even with a mere 4 corrupted landmarks out of a total of 8 * 168 = 1344, we
# can clearly see that contam_l2, the second image, looks slightly
# different from all the others, especially near the top of the image.

par(oldpar)

GeodRegr documentation built on Sept. 5, 2021, 5:17 p.m.