write.beast

Export treedata object to BEAST NEXUS file. This function was adopted and modified from ape::write.nexus

Usage

write.beast(treedata, file = "", translate = TRUE, tree.name = "UNTITLED")

Arguments

treedata

treedata object

file

output file. If file = "", print the output content on screen

translate

whether translate taxa labels

tree.name

name of the tree

Value

output file or file content on screen

Author

Guangchuang Yu

Examples

nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
write.beast(nhx)
#> #NEXUS
#> [R-package treeio, Fri Aug 25 06:57:03 2023]
#> 
#> BEGIN TAXA;
#> 	DIMENSIONS NTAX = 16;
#> 	TAXLABELS
#> 		Prayidae_D27SS7@2825365
#> 		Kephyes_ovata@2606431
#> 		Chuniphyes_multidentata@1277217
#> 		Apolemia_sp_@1353964
#> 		Bargmannia_amoena@263997
#> 		Bargmannia_elongata@946788
#> 		Physonect_sp_@2066767
#> 		Stephalia_dilata@2960089
#> 		Frillagalma_vityazi@1155031
#> 		Resomia_ornicephala@3111757
#> 		Lychnagalma_utricularia@2253871
#> 		Nanomia_bijuga@717864
#> 		Cordagalma_sp_@1525873
#> 		Rhizophysa_filiformis@3073669
#> 		Hydra_magnipapillata@52244
#> 		Ectopleura_larynx@3556167
#> 	;
#> END;
#> BEGIN TREES;
#> 	TRANSLATE
#> 		1	Prayidae_D27SS7@2825365,
#> 		2	Kephyes_ovata@2606431,
#> 		3	Chuniphyes_multidentata@1277217,
#> 		4	Apolemia_sp_@1353964,
#> 		5	Bargmannia_amoena@263997,
#> 		6	Bargmannia_elongata@946788,
#> 		7	Physonect_sp_@2066767,
#> 		8	Stephalia_dilata@2960089,
#> 		9	Frillagalma_vityazi@1155031,
#> 		10	Resomia_ornicephala@3111757,
#> 		11	Lychnagalma_utricularia@2253871,
#> 		12	Nanomia_bijuga@717864,
#> 		13	Cordagalma_sp_@1525873,
#> 		14	Rhizophysa_filiformis@3073669,
#> 		15	Hydra_magnipapillata@52244,
#> 		16	Ectopleura_larynx@3556167
#> 	;
#> 	TREE * UNTITLED = [&R] (((1[&Ev=S,ND=0,S=58]:0.0682841,(2[&Ev=S,ND=1,S=69]:0.0193941,3[&Ev=S,ND=2,S=70]:0.0121378)[&Ev=S,ND=3,S=60]:0.0217782)[&Ev=S,ND=4,S=36]:0.0607598,((4[&Ev=S,ND=9,S=31]:0.11832,(((5[&Ev=S,ND=10,S=37]:0.0144549,6[&Ev=S,ND=11,S=38]:0.0149723)[&Ev=S,ND=12,S=33]:0.0925388,7[&Ev=S,ND=13,S=61]:0.077429)[&Ev=S,ND=14,S=24]:0.0274637,(8[&Ev=S,ND=15,S=52]:0.0761163,((9[&Ev=S,ND=16,S=53]:0.0906068,10[&Ev=S,ND=17,S=54]:1e-06)[&Ev=S,ND=18,S=45]:1e-06,((11[&Ev=S,ND=19,S=65]:0.120851,12[&Ev=S,ND=20,S=71]:0.133939)[&Ev=S,ND=21,S=56]:1e-06,13[&Ev=S,ND=22,S=64]:0.0693814)[&Ev=S,ND=23,S=46]:1e-06)[&Ev=S,ND=24,S=40]:0.0333823)[&Ev=S,ND=25,S=35]:1e-06)[&Ev=D,ND=26,S=24]:0.0431861)[&Ev=S,ND=27,S=19]:1e-06,14[&Ev=S,ND=28,S=26]:0.22283)[&Ev=S,ND=29,S=17]:0.0292362)[&Ev=D,ND=8,S=17]:0.185603,(15[&Ev=S,ND=5,S=16]:0.0621782,16[&Ev=S,ND=6,S=15]:0.332505)[&Ev=S,ND=7,S=12]:0.185603)[&Ev=S,ND=30,S=9];
#> END;