Compute distance matrix from bases.

Compute distance matrix from bases.

path_dist(history)

Arguments

history

history of the plots

Examples

# This code is to be used as an example but you should increase
# the max from 2 to 50, say, to check tour coverage.
flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
grand <- interpolate(save_history(flea_std, max = 2), 0.2)
# The grand tour  -----------------------------
# Look at the tour path in a tour, how well does it cover a sphere
# Using MDS to summarise the high-d space of projections
# Last basis is a duplicate, needs removing
d <- path_dist(grand[,,-dim(grand)[[3]]])
ord <- as.data.frame(MASS::isoMDS(d)$points)
#> initial  value 0.032035 
#> final  value 0.006293 
#> converged
require(ggplot2)
ggplot(data = ord, aes(x=V1, y=V2)) +
  geom_path() +
  coord_equal() +
  labs(x = NULL, y = NULL)


# Compare five guided tours  -----------------------------
holes1d <- guided_tour(holes(), 1)
tour_reps <- replicate(5, save_history(flea_std, holes1d, max = 2),
  simplify = FALSE
)
#> Value  1.175   161.5 % better  - NEW BASIS
#> Value  1.256   124.2 % better  - NEW BASIS
#> Value  1.099   161.1 % better  - NEW BASIS
#> Value  1.191   8.7 % better  - NEW BASIS
#> Value  0.969   72.9 % better  - NEW BASIS
tour_reps2 <- lapply(tour_reps, interpolate, 0.2)

bases <- unlist(lapply(tour_reps2, as.list), recursive = FALSE)
class(bases) <- "history_list"
index_values <- paths_index(tour_reps2, holes())
index_values$step <- index_values$step.1
d <- path_dist(bases)
ord <- as.data.frame(cmdscale(d, 2))

info <- cbind(ord, index_values)
ggplot(data = info, aes(x = step, y = value, group = try)) +
  geom_line()
#> Don't know how to automatically pick scale for object of type <function>.
#> Defaulting to continuous.
#> Error in geom_line(): Problem while computing aesthetics.
#> ℹ Error occurred in the 1st layer.
#> Caused by error in `compute_aesthetics()`:
#> ! Aesthetics are not valid data columns.
#> ✖ The following aesthetics are invalid:
#> ✖ `x = step`
#> ℹ Did you mistype the name of a data column or forget to add `after_stat()`?
##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
##  geom_path() +
##  geom_point(aes(size = value)) +
##  coord_equal()
##last_plot() + facet_wrap(~try)