R Under development (unstable) (2024-08-17 r87027 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RPointCloud)
> library(TDA)
> set.seed(54321)
> theta <- seq(0, 359, by = 8) * pi/180
> L <- length(theta)
> x <- cos(theta) + rnorm(L, 0, 0.2)
> y <- sin(theta) + rnorm(L, 0, 0.2)
> z <- matrix(rnorm(2*L, 1, 0.5), ncol = 2)
> joint <- rbind(as.matrix(data.frame(x, y)), z)
> joint <- rbind(joint, joint[1:2,]) # deliberately duplicate data rows in longest loop
> eucd <- dist(joint)
> 
> eucrip <- ripsDiag(eucd, maxdimension=1, maxscale = 3,
+                    dist = "arbitrary", library = "Dionysus",
+                    location = TRUE)
> ripper <- ripsDiag(joint, maxdimension=1, maxscale = 3,
+                    dist = "euclidean", library = "Dionysus",
+                    location = TRUE)
> RD <- ripper$diagram
> oneD <- RD[,1] == 1
> duration <- RD[oneD, 3] - RD[oneD,2]
> w <- which.max(duration)
> 
> dexter <- disentangle(ripper, joint)
> cyc1 <- Cycle(dexter, 1, 13, "blue") # fails with an error in RPointCloud 0.3.0
> ## possibly worse, it gives the wrong answer in 0.3.1 - 0.3.4
> plot(cyc1, joint) # note the awful picture in 0.3.4!!
> 
> cyc2 <- Cycle(eucrip, 1, 13, "purple")
> plot(cyc2, joint)
> 
> ifelse (all(cyc1@index == cyc2@index), # should be true
+         "FIXED",
+         "BROKEN")
[1] "FIXED"
> 
> 
> proc.time()
   user  system elapsed 
   5.09    0.54    5.62