Rmarkdowns in examples don't work

[davidecrs]

Hi,

I cloned the repo and tried to run the examples as they are without changing them, but they don't work.

1. In the mnist_example.Rmd for the following step

m2 <- mapper2D(distance_matrix = mnist_distances,
                filter_values = list(emb@data@data[,1], emb@data@data[,2]),
                num_intervals = c(30,30),
                percent_overlap = 35,
                num_bins_when_clustering = 10);

I get the following error:
Error in vertices_in_level[[k1]] : subscript out of bounds

2. Regarding the vr_cycle_example.Rmd in the last line of code

(scores[order(scores$R1, scores$R0),])[1:5,]

I get the following error
Error in order(scores$R1, scores$R0) : argument 1 is not a vector

In this case seems that scores doesn't have R1

> head(scores)
                     R0    p0        q0
0610007P14Rik 1.0076786 0.323 0.5204212
0610009O20Rik 0.9974801 0.201 0.3855278
0610010F05Rik 0.7698217 0.000 0.0000000
0610010K14Rik 0.9990372 0.203 0.3884544
0610011F06Rik 0.9924835 0.132 0.2933002
0610037L13Rik 0.9924345 0.130 0.2901680

OS: Ubuntu 20.04.2 LTS
R version 4.1.0 (2021-05-18)

[govekk]

The first issue is an error in a function from a different package, TDAmapper. I was able to reproduce this error when I installed TDAmapper from CRAN, rather than from the GitHub paultpearson/TDAmapper. In one of their issues, they suggest using the GitHub version since the CRAN version is out of date (paultpearson/TDAmapper#6 (comment)). I was able to fix this error by removing the CRAN version and installing the GitHub version:

remove.packages(TDAmapper)
devtools::install_github(paultpearson/TDAmapper)

And then restarting R.

The second issue was a simple fix - we updated the one_forms parameter default of rayleigh_selection() from TRUE to FALSE, but that function call in the example expects one_forms=TRUE. I have updated the example to explicitly set that parameter.