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Code improvements #52
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Thank you @danielnachun everything you said sound good to me.
should, or should not?
My version of susieR should be merged to stephenslab susieR hopefully soon depending on progress of the other project. However I can also merge the prototype as is without loudly advertising the feature, just to save us some logistics headache. i can push through on getting mr.ash and mr.mash on cran before our official release.
Sounds good. I wonder who could take care of this -- Travyse and/or Tiffany?
I'm not particularly familiar with these tbh but sounds doable. The question is how to implement it. Perhaps we should wait until we have enough unit tests, then someone (who?) would have to identify each of it, rewrite, and run though the tests? |
Now that our package has draft implementations of most major steps, we should start to think about polishing the code more to emphasize simplicity, readability and consistency. Broadly speaking I think we should prioritize our choice of packages to use functions from sources in the following order:
The following packages that we currently depend on can probably be removed
Rlab
- uses amessage2
function that is not even in the documentation - can we just use the basemessage
function?doMC
,doParallel
andforeach
- all of these can be replaced with a combination of tidyverse packages:future
,dplyr
andpurrr
.data.table
- thefread
function can be replaced with thevroom
function from thevroom
package.plink2R
- this can be replaced withsnpStats
for loading bed/bim/fam files andpgenlibr
The following packages are currently only available on GitHub. We cannot submit our package to CRAN or Bioconductor until these packages have been made available on one of those two resources:
susieR
mr.mash.alpha
mr.ash.alpha
Stylistically, I would like to also strictly enforce several concepts from functional programming:
group_modify
orgroup_map
fromdplyr
when working with data frames, andmap
(or its derivates) frompurrr
when working with listsThe text was updated successfully, but these errors were encountered: