Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = ">"
)
## ----load----------------------------------------------------------------
# load TDAstats
library("TDAstats")
# load unif2d dataset
data("unif2d")
## ----calcpc, fig.height = 4.5, fig.width = 6-----------------------------
# calculate persistent homology
data.phom <- calculate_homology(unif2d)
# visualize persistent homology
plot_barcode(data.phom)
## ----calcdist------------------------------------------------------------
# calculates the distance between two points
calc.dist <- function(point1, point2) {
sqrt(sum((point1 - point2) ^ 2))
}
# calculates a distance matrix for a point cloud
calc.distmat <- function(point.cloud) {
# create empty matrix
ans.mat <- matrix(NA, nrow = nrow(point.cloud), ncol = nrow(point.cloud))
# populate matrix
for (i in 1:nrow(point.cloud)) {
for (j in 1:nrow(point.cloud)) {
ans.mat[i, j] <- calc.dist(point.cloud[i, ], point.cloud[j, ])
}
}
# return distance matrix
return(ans.mat)
}
## ----calcdistmat, fig.height = 4.5, fig.width = 6------------------------
# calculate distance matrix for unif2d
dist.unif2d <- calc.distmat(unif2d)
# calculate persistent homology using distance matrix
dist.phom <- calculate_homology(dist.unif2d, format = "distmat")
# visualize persistent homology
plot_barcode(dist.phom)
## ----plotcmp, fig.height = 2.6, fig.width = 3.4, fig.show = "hold"-------
# plot barcode for point cloud
plot_barcode(data.phom)
# plot barcode for distance matrix
plot_barcode(dist.phom)
## ----checkidentical------------------------------------------------------
identical(data.phom, dist.phom)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.