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Came up in this discussion - several summaries I tried fail due to bladj issues - when I'm not clear on why bladj was needed!
Is it possible to summarize the datelife result without requiring it?
e.g.
> queryTree <- "((Psittirostra_psittacea:16.17084019,(((((((((Hemignathus_affinis:0.205878784,Viridonia_sagittirostris:0.2058788809)NA:0.6176362992,Hemignathus_hanapepe:0.82351501)NA:0.82351501,Hemignathus_wilsoni:1.64703)NA:1.64703,(Chlorodrepanis_virens:1.64703,Chlorodrepanis_stejnegeri:1.64703)mrcaott324560ott667189:1.64703)mrcaott324560ott324561:1.64703,((Akialoa_stejnegeri:1.2352725,Akialoa_obscura:1.235272524)NA:1.2352725,Chlorodrepanis_flava:2.470545)mrcaott324558ott706153:2.470545)mrcaott324558ott324560:1.64703,(((Drepanis_coccinea:1.64703,(Himatione_sanguinea:0.823515,Himatione_fraithii:0.8235151401)NA:0.823515)mrcaott298780ott823302:1.64703,Palmeria_dolei:3.29406)mrcaott298765ott298780:1.64703,(Loxops_mana:2.470545,Loxops_ochraceus:2.47054503)NA:2.470545)mrcaott298765ott298768:1.64703)mrcaott298765ott324558:1.647029,(((Loxops_caeruleirostris:2.058787,Loxops_coccineus:2.058787)mrcaott1016648ott1089641:2.058787,Pseudonestor_xanthophrys:4.117574)mrcaott823300ott1016648:2.058787,Magumma_parva:6.176361)mrcaott823300ott1089642:2.058788)mrcaott298765ott823300:1.64703,(Telespiza_cantans:6.58812,Loxioides_bailleui:6.58812)mrcaott213516ott221897:3.294059)mrcaott157614ott298765:1.64703,((((Paroreomyza_maculata:1.441151027,Rhodacanthis_palmeri:1.441151164)NA:1.441151027,Paroreomyza_montana:2.882302)NA:1.441151,Paroreomyza_flammea:4.32345312)NA:1.441151,Oreomystis_bairdi:5.764604)mrcaott298769ott823298:5.764605)mrcaott157614ott298769:4.641631)mrcaott6366ott157599:1.540082,Chloridops_kona:17.71092218)mrcaott6366ott88283:1;"
> bird_query = datelife::make_datelife_query(input = queryTree)
> phylo_sdm <- datelife::datelife_search(input = bird_query,
summary_format = "phylo_sdm")
... Running a DateLife search.
... Searching DateLife's OpenTree chronogram database version v2023.12.30
Search done!
Input taxon names were found in 8 chronograms.
Trying with overlap = 2
Success!
1 out of 8 chronograms tried: Failed.
2 out of 8 chronograms tried: Ok.
3 out of 8 chronograms tried: Ok.
4 out of 8 chronograms tried: Ok.
5 out of 8 chronograms tried: Failed.
6 out of 8 chronograms tried: Failed.
7 out of 8 chronograms tried: Ok.
8 out of 8 chronograms tried: Failed.
Synthesizing 4 chronograms with SDM
Warning in check_root_node(phylo, ages) :
bladj may fail; the root node 'n1' is not in the ages nodes
Error: Program '/home/ejmctavish/R/x86_64-pc-linux-gnu-library/4.3/phylocomr/bin//phylocom' terminated by SIGNAL (Segmentation fault)
The text was updated successfully, but these errors were encountered:
Came up in this discussion - several summaries I tried fail due to bladj issues - when I'm not clear on why bladj was needed!
Is it possible to summarize the datelife result without requiring it?
e.g.
The text was updated successfully, but these errors were encountered: