From c04c7d3ac32f9db4dbe690b8b9a04bae9e1b262e Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Thu, 28 Dec 2023 18:41:02 -0500 Subject: [PATCH] Add note about exluding genus data from node_data when importing with the ltp function. --- inst/scripts/get_living_tree_2023.R | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/inst/scripts/get_living_tree_2023.R b/inst/scripts/get_living_tree_2023.R index 26d598f..cb271e4 100644 --- a/inst/scripts/get_living_tree_2023.R +++ b/inst/scripts/get_living_tree_2023.R @@ -248,6 +248,12 @@ node_data_extended$node <- match(node_data$node_label, tree_extended$node.label) sum(tree_extended$node.label[node_data_extended$node - Ntip(tree_extended)] == 'NA') tree_extended$node.label[23504 - Ntip(tree_extended)] == '2157' +## note that node_data_extended, only contains data about genera with +## two or more tips, i.e. I could get a MRCA. The rest are only tips. +## It's probably better to filter out genera from node_data when +## importing with the ltp function and use only the tips for managing +## genus information. + # Export data ------------------------------------------------------------- tree_fname <- file.path('inst', 'extdata', 'LTP_all_08_2023.newick') # ape::write.tree(tree, tree_fname)