Flipping misc organisation to address #107

[gregorgorjanc]

Here is an implementation where we flip misc organisation from ind-node to node-ind for simplicity and speed of operations. As discussed in #107.

Looking forward to feedback;)

[gregorgorjanc]

The last commit is just an exploration of how this new org would work if we use Pop or MultiPop in misc

[gaynorr]

The family pulled me away, so I just pushed something that is incomplete. I tried to add a length method to MultiPop, but it isn't working. Also, the mergePop is failing in the tests inside the testthat tests.

[gregorgorjanc]

Yes, the test is unfinished because I wasn't sure/clear if we want to handle Pop or MultiPop in the new misc organisation. I initiated three cases:

  pop@misc$mtP = popOrig
  pop@misc$mtLP = list(popOrig, popOrig)
  pop@misc$mtMP = multiPop

Note that pop@misc$mtLP (list of Pop) is effectively the same as pop@misc$mtMP (MultiPop) and I think this is how we should move onwards - working with these options.

I was not sure if you wanted to have support for pop@misc$mtP (Pop) as well, but this is a less natural use case (subsetting the misc that contains pop as one of the misc-list-nodes would pick individuals of the population), though we can make it work by developing a length(method) for Pop too (making it the same to nInd()), I think.

[gregorgorjanc]

I have just tested the length() method on MultiPop and it works as expected!

> length(multiPop)
[1] 2

[gregorgorjanc]

This last push makes all the tests run. There is just one test commented out since we cannot create an empty MultiPop. Might add that later in another issue/PR - #169

[gaynorr]

I think I know how to fix this. It should just be a matter of changing the validity function for MultiPop. It's currently a loop with 1:length(object@pops). This fails when length is 0. I should instead be using seq_along(length(object@pops)), because it works when the value is zero. This is a best practice for R programming that I didn't know about until relatively recently.