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Error in phylo_median #94

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snacktavish opened this issue Apr 23, 2024 · 1 comment
Open

Error in phylo_median #94

snacktavish opened this issue Apr 23, 2024 · 1 comment

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@snacktavish
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snacktavish commented Apr 23, 2024

> spp = c("Caprimulgus aegyptius","Vanellus tricolor","Recurvirostra americana","Centropus nigrorufus","Bombycilla cedrorum","Orthotomus cinereiceps","Ortygospiza atricollis", "Nasica longirostris","Terpsiphone viridis", "Myiothlypis signata","Atlapetes melanopsis","Idiopsar brachyurus","Rauenia bonariensis","Lessonia oreas","Tyrannus niveigularis"  ,"Rukia longirostra","Zosterops ponapensis","Ixobrychus involucris","Melanerpes pulcher","Picus viridanus")
> bird_query = datelife::make_datelife_query(input = spp)
---> Phylo-processing 'input'.
* 'input' is not a phylogeny.
---> Making a DateLife query.
---> Runnning TNRS to match input names to reference taxonomy (OTT).
  |=====================================================================================================================================================================| 100%
---> Working with the following 20 taxa: Caprimulgus aegyptius | Vanellus tricolor | Recurvirostra americana | Centropus nigrorufus | Bombycilla cedrorum | Orthotomus cinereiceps | Ortygospiza atricollis | Nasica longirostris | Terpsiphone viridis | Basileuterus signatus... omitted  10 taxon names.
DateLife query done!

> phylo_median <- datelife::datelife_search(input = bird_query,
+                                           summary_format = "phylo_sdm")
... Running a DateLife search.
... Searching DateLife's OpenTree chronogram database version v2022.01.28
Search done!

Input taxon names were found in 6 chronograms.
Trying with overlap = 2

Success!

1 out of 6 chronograms tried:  Ok.
2 out of 6 chronograms tried:  Ok.
3 out of 6 chronograms tried:  Ok.
4 out of 6 chronograms tried:  Ok.
5 out of 6 chronograms tried:  Ok.
6 out of 6 chronograms tried:  Ok.

 Synthesizing 6 chronograms with SDM
... No target_tree was provided, obtaining a tree topology from Open Tree synthetic phylogeny.
  |=====================================================================================================================================================================| 100%
Error in if (is.numeric(input$ott_id) & !is.na(input$ott_id)) { : 
  the condition has length > 1```
@snacktavish
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I think this is fixed in https://github.com/LunaSare/datelife. Needs to be merged!

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