How to run ptR?

[AvonDeng]

hello, I have installed ptR package. But I don't know how to calculate the number of path. Can you give an example? In order to know how to use it. Thank you very much！

[gertjanssenswillen]

Hi, what is the format your process tree is in?

[AvonDeng]

The process trees were generated using the framework in https://github.com/tjouck/PTandLogGenerator. This tool generates both newick and PTML formats.

In your ptR package, there is a TREE.ptml file, but I don't know how to use this file to get the number of paths. Sorry, I'm new to R language.

[gertjanssenswillen]

No problem, this project is not longer under active development, and the documentation is missing.

First of all, you need to install the original code (initial commit), you can do this as follows with devtools:

devtools::install_github("gertjanssenswillen/ptR", ref = "8780b3d3964571d6db777c349be3504c1e2fa68c")
Then you can load the package.
library(ptR)
newick files can be read with process_tree, and the number of paths can be computed with number_of_paths

number_of_paths(process_tree("newick_file.nw"))
Please let me know whether this works for you. Feel free to contact me by email (gert.janssenswillen@uhasselt.be), if you want to use this functionality for your work. In that case I might consider adding some documentation and fixing some issues.

[AvonDeng]

Ok, I tried it a few times. It didn't work out. And the number of paths returned was 0 or error: index out of bounds. I'm not sure whether the format of newick files are wrong or other issues. Thank you!

[gertjanssenswillen]

Could you send me your newick file by mail? Then I'll try to find the bug.

[AvonDeng]

I have solved the problem. The reason is the 'p_redo' and 'xor_probabilities' variables have no value. Thank you for your answer！