S3 object HospiNet

[PascalCrepey]

We need to build an S3 object, let's call it HospiNet, which will contain the hospital matrix and relevant indicators (see vignette for details). This object should have a dedicated summary and print method.

[PascalCrepey]

Just created a constructor for this S3 object but no generic method yet...

[nolwenn]

Why do you have matrix and edgelist in your object?

[PascalCrepey]

Well, sometimes we need the matrix (in spreading simulation) and sometimes we need the edgelist (for igraph), so since both are created at one point I thought we could keep them both and let the user choose what he/she wants...

[nolwenn]

But you have methods to go from one to the other, no? You might not want to store the two types in one object as it might take a lot of memory?

[PascalCrepey]

mydb = create_fake_patientDB(n_patients = 100000, n_hospital = 2500)
hnet = hospinet_from_patient_database(base = mydb, noloops = FALSE)
format(object.size(hnet), units = "Mb") #27.3Mb
format(object.size(mat$matrix), units = "Mb") #24.3Mb
format(object.size(mat$edgelist), units = "Mb") #3.1Mb

we'll know what to remove if we have a memory size issue... ;-)

[nolwenn]

Other question: should not we be able to apply the getMetrics, get_degree... functions on the HospiNet object and not on some igraph object only ?

[PascalCrepey]

Sure but that would mean either - having an igraph object within HospiNet (which raises the question you asked before about size efficiency - or doing the igraph converting at the getMetrics level (I think it's what I introduced in one of my last commits) - switch HospiNet from S3 to R6 and have an active field which would create the igraph on the fly if and when it's needed (maybe the best solution...) Le jeu. 1 août 2019 à 13:30, Nolwenn Le Meur <notifications@github.com> a écrit :

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[tjibbed]

I will need to do some reading up here on the difference between S3 and R6 objects, but the last option sounds like the best solution to me, indeed.

As for @nolwenn 's question, it seems most intuitive to be able to apply these functions on the HospiNet object.

[PascalCrepey]

I've implemented the R6 mechanism. You can see it at work at the end of the work-flow vignette (text of the vignette still needs to be updated...)

[tjibbed]

Brilliant. Hadn't noticed yet... I'm still catching/reading up after being away for a week and a half.