Remove sex

[janaobsteter]

Some functions use the sex information (createDrones) while others use caste information. We should probably decide:

• do we want both?
• which one to use in functions?

[gregorgorjanc]

Best to use caste everywhere I think and then we don’t advocate using sex at all!

[janaobsteter]

Do we still keep the sex info, just don't advocate it? Or remove it all together?

[gregorgorjanc]

I think we should remove it altogether. Caste implies sex too, so best to stick to that. But we need to be careful about this change as it will likely break many things.

We really should start adding tests!!! Let’s teach @JerBub and @LStrachan on how to build tests well as we have lots of functionality already and for every such major change I wonder what will work and what won’t!

[gregorgorjanc]

One example where code could be much simpler - using caste instead of sex in reducing drone haplotypes and genotypes - see https://github.com/HighlanderLab/SIMplyBee/issues/326

[janaobsteter]

Just making sure we are still implementing this, so that I don't mention it in the paper?

[gregorgorjanc]

Yes! We have caste. No need to make life more complex to also have sex in my view.

[janaobsteter]

I'll do this while I'm changing some other functions

[janaobsteter]

A question - do we then also want to change the "sex" parameter in functions to "caste"? All genome related functions use the "sex" somwhere in the function.

[gregorgorjanc]

Hmm! This could be tricky! Do all genome functions have the sex arg or just the calc* ones? In calculations we often need to know if genotypes come from haploid individuals (drone and father castes!) or diploid individuals! Maybe we need a utility isHaploid() function so that we can do those calculations?

[janaobsteter]

I will create a list of functions that use sex and we'll see what would be best

[janaobsteter]

We decided to keep this for the submission, since it's more complex than we've anticipated, but we don't want to mention it in the vignettes or the paper

[janaobsteter]

Where do we use sex:

• Level0: getCasteSex(), reduceDroneHaplo(), reduceDroneGeno(), getCsdAlleles(), getCsdGeno(), getIbdHaplo(), getQtlHaplo(), getQtlGeno(), getSegSiteHaplo(), getSegSIteGeno(), getSnpHaplo(), getSnpGeno(), getPooledGeno(), calcBeeGRMIbd(), calcBeeAlleleFreq(), calcBeeGrmIbd()
• Level1: createCastePop()

[gregorgorjanc]

Looks like you found a bug!!! Well done;)

[gregorgorjanc]

Hmm, the email notification had a different text! Are we missing droneHaplo arg in some genomics functions?

[janaobsteter]

Yeah,I realized I just overlooked it,all good!!!

[janaobsteter]

We decide to keep it for now due to computational use (saying "M" instead of "drones" and "fathers")