Do all summaries require bladj? #96
Description
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)