Timeline for phytools add.species.to.genus could not match your species to a genus
Current License: CC BY-SA 4.0
6 events
| when toggle format | what | by | license | comment | |
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| S Aug 9, 2023 at 13:02 | history | suggested | A. Bollans | CC BY-SA 4.0 |
clarify use of _
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| Aug 9, 2023 at 13:02 | comment | added | M__♦ | Thanks @A.Bollans thats good debugging. In tree files removing all blank space is standard practice, in phylip format this a bug. | |
| Aug 9, 2023 at 8:57 | vote | accept | A. Bollans | ||
| Aug 9, 2023 at 8:57 | review | Suggested edits | |||
| S Aug 9, 2023 at 13:02 | |||||
| Aug 9, 2023 at 8:55 | comment | added | A. Bollans |
I tried lots of different combinations of parameters but in the end the only thing that resolved the issue was using underscores instead of spaces in the tree labels i.e. test_tree$tip.label = c("t3_sp1", "t4_sp1", "t5_sp1", "t2_sp1", "t1_sp1"). Curiously though when the tip labels are set like this, the function works with species = "t1_polytome1" and species = "t1 polytome1". WRT (2), phytools::genus.to.species.tree(test_tree, "t1_polytome1") returned a tree without t1_polytome1 added and no error given, maybe because it expects a genus-level tree.
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| Aug 8, 2023 at 18:11 | history | answered | M__♦ | CC BY-SA 4.0 |