Imprinting new functions

[david20011999]

As we talked, here you have my pull request for check new imprinting functions before send to Chris pull request. You will find:

• [x] added TraitAI and TraitADI
• [x] new function in calcGenParam() called calcGenParamS() that is following Chris variance components estimation script. This functions work with and without dominance
• [x] removal of old calcGenParam() functions
• [x] modification of getGv() function. getGvA2() is working as before and a new function getGvS() is working for imprinting
• [x] id() is not working more with paternal and maternal deviations and examples were removed
• [x] testing has been changed to the new imprinting deviation status
• [x] a vignette I did few time ago, it should be reviwed but i've included it as a potential action
• [x] importTrait() for ADI and AI
• [x] allow to import 1segsite with importHaplo()
• [x] adaptation of genParam()

Future and potential steps:

• [ ] I think I've changed functions explanation but perhaps something is missing
• [ ] Develop documentation for new functions and functionalities (for man directory)
• [ ] Poliploids
• [ ] Improve vignette
• [ ] ADEI,...
• [ ] More parameters or information needed?

[david20011999]

Simulating an imprinted and a non-imprinted trait, when bv() function is required, originates a bug. This is due to the fact that lines 534 and 538 of popSummary.R are substituing bv to imprinting bv in all traits, not just the imprinted trait. To fix this, ret[sel, ] has to be changed to ret[sel, impTest]. I have done it in my computer version, I will upload it to my github as soon as possible.

[gregorgorjanc]

@david20011999 i have fallen behind in this work of yours! Sorry. We need to start looking at this during our meetings. Please put it on our agenda. Maybe we will also have to start meeting more regularly.

I think that the 1seg site change should best be submitted as a PR right away to Chris’s repository upstream - that is not related to imprinting. Please do that - fork a fresh upstream, clone it, modify it, push, and open a PR for Chris to revise.