betta_posthoc() fails with breakaway v4.8.5 (missing value where TRUE/FALSE needed)

[AlexaBennett]

After updating breakaway to v4.8.5, I encountered the following error when running DivNet::betta_posthoc():

Error in `if (k2 == 0) ...`:
! missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. └─DivNet::betta_posthoc(betta_results, shannon_estimates)
 2.   └─DivNet:::generate_cld(pvals, alpha, letter_set)
 3.     └─multcompView::multcompLetters(pvals, threshold = alpha, Letters = letter_set)

Additional details:

Works as expected with when rolled back to adw96/breakaway@4c03e5acf3f54bb169a236990712663bf5eb9f4d
Fails with breakaway 4.8.5
DivNet version: 0.4.1
R version: 4.4.0 on HPC

[svteichman]

Hi @AlexaBennett, are you able to include a minimal reproducible example of this error? I checked our internal tests with betta_posthoc() and didn't see a clear error after updating to breakaway 4.8.5. If you could provide a script with this error and the data that is used then I can look into what is causing this error!

[rgtaketani]

Hi all,

I had a similar issue. I dig a bit and found that betta_lim was generating very low p-values with < on it. Thus, line 139 (dplyr::mutate(p_value = as.numeric(p-values)) %>%) generate a blank value. So, I modified to dplyr::mutate(p_value = as.numeric(gsub("< ", "", p-values))) that fixed everything.
I hope this is helpful.