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comparison EstimEndem.R @ 1:f3a977826375 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit cbd0cb48be9f2aa5e30c917d6a9031ef1a7a83c8
author ecology
date Thu, 05 Jun 2025 16:50:45 +0000
parents f7a55ccf2a3e
children
comparison
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0:f7a55ccf2a3e 1:f3a977826375
41 #select the less distorting clustering method, best fitting between phylogenetic distances in phylobeta matrix 41 #select the less distorting clustering method, best fitting between phylogenetic distances in phylobeta matrix
42 # and raw distances from branch lengths of the tree 42 # and raw distances from branch lengths of the tree
43 select_linkage(phylo_beta[[1]]) 43 select_linkage(phylo_beta[[1]])
44 44
45 #select optimal number of clusters with selected method 45 #select optimal number of clusters with selected method
46 optim <- optimal_phyloregion(phylo_beta[[3]], k = 30) 46 optim <- optimal_phyloregion(phylo_beta[[3]])
47 print(paste("the best number of cluster is :", optim$optimal$k)) 47 print(paste("the best number of cluster is :", optim$optimal$k))
48 #plot(optim$df$k, optim$df$ev, pch = 20) # k - nbr of clusters VS explained variance given k 48 #plot(optim$df$k, optim$df$ev, pch = 20) # k - nbr of clusters VS explained variance given k
49 # k has to be selected by a user 49 # k has to be selected by a user
50 50
51 # pass the grid cell to spatial format 51 # pass the grid cell to spatial format