Occasional error during resampling

[HS6986]

Dear Professor Smith,

I am using TreeSearch v1.5.1 for analyzing morphological datasets using my custom R scripts (sorry for the mess), which were adapted from phylo-workflow. During analysis, while performing jackknife resampling, execution occasionally stops with the following error (it usually does not happen and execution completes without problems).

Error in if (nTip < length(dataset)) { : 
  missing value where TRUE/FALSE needed

I don't know if there is a problem with my code or with TreeSearch's code, but I would appreciate it if you could review the issue.

[ms609]

Thanks for the report, and sorry to hear you're encountering this error!
To investigate, it would be helpful to run these scripts myself and reproduce the error – would you be willing to share your matrix file, either here or by e-mail (to martin.smith at durham.ac.uk)?

[HS6986]

Sure! I am reanalyzing the morphological dataset from Raeker et al. (2025) with a constraint for the monophyly of Priapulida, following the results of Howard et al. (2022) (unfortunately, this reanalysis doesn't seem to yield particularly interesting results). For these data only, the error seems to consistently occur during jackknife resampling.

Here's the folder containing the matrix, the constraint file, and the R scripts). I am using R v4.4.2 for the analysis.

[ms609]

That's great, thanks. I've determined the cause of the error, which will be fixed by #174.
You can install the patched version of the package (v1.5.1.9003) with devtools::install_github("ms609", "TreeSearch").

[HS6986]

Thank you for your prompt response and fixing the bug so quickly. I'm glad I could be of help.