added example for oaks with ZIPLN

PLN-team · Sep 10, 2024 · 1e3b8e5 · 1e3b8e5
1 parent 859031a
commit 1e3b8e5
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/inst/case_studies/oaks_tree.R b/inst/case_studies/oaks_tree.R
@@ -97,14 +97,16 @@ factoextra::fviz_pca_biplot(
 
 ## Network inference with sparce covariance estimation
 
-system.time(myZIPLNnets <- ZIPLNnetwork(Abundance ~ 0 + tree + offset(log(Offset)), zi = "single", data = oaks, control = ZIPLNnetwork_param(min_ratio = 0.1)))
-
 system.time(myPLNnets <- PLNnetwork(Abundance ~ 0 + tree + offset(log(Offset)), data = oaks, control = PLNnetwork_param(min_ratio = 0.1)))
 plot(myPLNnets)
 plot(getBestModel(myPLNnets, "EBIC"))
 # stability_selection(myPLNnets)
 # plot(getBestModel(myPLNnets, "StARS", stability = .975))
 
+system.time(myZIPLNnets <- ZIPLNnetwork(Abundance ~ 0 + tree + offset(log(Offset)), zi = "single", data = oaks, control = ZIPLNnetwork_param(min_ratio = 0.1)))
+plot(myZIPLNnets)
+plot(getBestModel(myZIPLNnets, "EBIC"))
+
 ## Mixture model to recover tree structure
 system.time(my_mixtures <- PLNmixture(Abundance ~ 1 + offset(log(Offset)), data = oaks, clusters = 1:5))