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Add StARS selection criteria to PLN network #5

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mahendra-mariadassou opened this issue Mar 16, 2018 · 2 comments
Closed

Add StARS selection criteria to PLN network #5

mahendra-mariadassou opened this issue Mar 16, 2018 · 2 comments
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@mahendra-mariadassou
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Add a stability selection step by default (with a limited number of resamples) and update getBestModel to output network with StARS selected lambda.

@mahendra-mariadassou mahendra-mariadassou self-assigned this Mar 16, 2018
@jchiquet
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jchiquet commented May 8, 2018

I started a branch to implementing feature

@jchiquet
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jchiquet commented May 9, 2018

Done and inserted in the vignette of PLNnetwork. Here is a small example (note that the stability seleciton is performed only once)

library(PLNmodels)
library(ade4)
data("trichometeo")

abundance <- as.matrix(trichometeo$fau)

fits <- PLNnetwork(abundance)
network_StARS_.9  <- fits$getBestModel("StARS", stability = 0.9 )
network_StARS_.95 <- fits$getBestModel("StARS", stability = 0.95)
par(mfrow=c(1,2))
network_StARS_.9$plot_network()
network_StARS_.95$plot_network()

@jchiquet jchiquet closed this as completed May 9, 2018
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