Where are OGT, doubling time in mircoTrait output?

[jlw-ecoevo]

Hi!

I've got microTrait running with no issues but I am trying to find certain output variables and the output does not quite correspond to what it says in the README (e.g., no field called "all_traits"). None of the 3 granularity matrices seem to include OGT or min doubling time? (and this causes issues with the downstream analysis code)

Thanks! -JL

[ukaraoz]

Hi JL, thanks for letting me know, I should have made a mistake in pushing the local branch. Unfortunately, I am away for a few weeks and won't be able to get to this till then.

[michoug]

Hi, Any news on the implementation of these parameters in the package? Greg

[MarineBergot]

Hi, i have the same issues than most of people here (this one + the one with parallel), an update is possible ? your package is really cool and it would be super cool to use it if you have good version then we don't need to rewrite all your code! and same the dbcan database is now in v11 but it's hard to change everything as there is no option! thanks for your work!

[bryantdo]

any update on these issues

[ukaraoz]

These (mingentime and OGT) have been refactored into the current master branch.

[bryantdo]

Hello,

Still having this issue:

trait_matrixatgranularity3 = genomeset_results[["trait_matrixatgranularity3"]] %>% dplyr::select(c("id", traits, "mingentime", "ogt")) %>%

dplyr::slice(1:100) %>%

dplyr::filter(mingentime < 100) %>% dplyr::filter(!is.na(mingentime) & !is.na(ogt)) Error in dplyr::select(): ! Can't subset columns that don't exist. ✖ Column mingentime doesn't exist.

Any ideas?

[michoug]

Hi @bryantdo The names apparently changed to growthrate and optimumT Best Greg

[bryantdo]

@michoug Well thank you for that information!