Mercurial > repos > ecology > estimate_endem

diff 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
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--- a/EstimEndem.R	Tue May 20 09:52:29 2025 +0000
+++ b/EstimEndem.R	Thu Jun 05 16:50:45 2025 +0000
@@ -43,7 +43,7 @@
   select_linkage(phylo_beta[[1]])
   
   #select optimal number of clusters with selected method
-  optim <- optimal_phyloregion(phylo_beta[[3]], k = 30)
+  optim <- optimal_phyloregion(phylo_beta[[3]])
   print(paste("the best number of cluster is :", optim$optimal$k))
   #plot(optim$df$k, optim$df$ev, pch = 20)  # k - nbr of clusters VS explained variance given k
   # k has to be selected by a user