我已经生成了一棵树，但我很难将它植根于“猿”，而且我不确定我指定外群的方法是否正确。
以下是物种列表：
Agaricus_silvicola
Amanita_citrina
Amanita_echinocephala
Amanita_fulva
Amanita_pantherina
Amanita_phalloides
Amanita_rubescens
Amanita_strobiliformis
Amanita_vaginata
Amanita_virosa
Ampulloclitocybe_clavipes
Xerocomellus_chrysenteron
Boletus_edulis
Boletus_erythropus
Boletus_luridiformis
Boletus_luridus
Boletus_subtomentosus
Cantharellus_cibarius
Craterellus_tubaeformis
Clitocybe_fragrans
Infundibulicybe_geotropa
Clitocybe_gibba
Clitocybe_nebularis
Clitocybe_odora
Clitocybe_phyllophila
Clitocybe_vibecina
Clitopilus_prunulus
Coprinus_silvaticus
Cortinarius_anomalus
Cortinarius_decipiens
Cortinarius_flexipes
Cortinarius_hemitrichus
Cortinarius_hinnuleus
Craterellus_cornucopioides
Cystolepiota_seminuda
Geastrum_fimbriatum
Geastrum_triplex
Gymnopus_androsaceus
Gymnopus_confluens
Gymnopus_dryophilus
Gymnopus_peronatus
Hebeloma_crustuliniforme
Hebeloma_leucosarx
Hebeloma_mesophaeum
Hebeloma_sacchariolens
Hemimycena_cucullata
Hydnum_repandum
Inocybe_assimilata
Inocybe_asterospora
Inocybe_bongardii
Inocybe_flocculosa
Inocybe_fraudans
Inocybe_geophylla
Inocybe_lacera
Inocybe_napipes
Inocybe_petiginosa
Inocybe_rimosa
Laccaria_laccata
Lactarius_azonites
Lactarius_piperatus
Lactarius_sphagneti
Lactarius_tabidus
Lactarius_vellereus
Lactarius_zonarius
Lepiota_castanea
Lepiota_cristata
Lepista_flaccida
Lepista_nuda
Lycoperdon_molle
Lycoperdon_nigrescens
Lycoperdon_perlatum
Macrocystidia_cucumis
Marasmius_cohaerens
Marasmius_epiphyllus
Marasmius_wynneae
Mutinus_caninus
Mycena_metata
Mycena_pelianthina
Mycena_polyadelpha
Mycena_rosella
Mycena_vitilis
Paxillus_involutus
Phallus_impudicus
Psathyrella_obtusata
Pseudoclitocybe_cyathiformis
Rhodocollybia_butyracea
Rhodocollybia_maculata
Russula_aeruginea
Russula_atropurpurea
Russula_cyanoxantha
Russula_delica
Russula_foetens
Russula_fragilis
Russula_heterophylla
Russula_nigricans
Russula_ochroleuca
Russula_rosea
Russula_virescens
Russula_xerampelina
Scleroderma_areolatum
Scleroderma_verrucosum
Stropharia_aeruginosa
Tricholoma_album
Tricholoma_fulvum
Tricholoma_ustale
Tubaria_conspersa
Tubaria_furfuracea
Tylopilus_felleus
Hymenopellis_radicata
我已经安装了很多包，但不完全确定我使用的是哪些包：
library(ggtree)
library(ggplot2)
library(motmot.2.0)
library(caper)
library(geiger)
library(ape)
library(MASS)
library(phytools)
library(adephylo)#
library(quantreg)#
library(phangorn)
library(rotl)
library(MuMIn)
读入数据：
data<- read.csv("filename.csv")
创建物种列表：
species.list <- as.character(levels(as.factor(data$unique_name)))
创建分类：
taxonomy <- tnrs_match_names(species.list[1:109], context_name = "Basidiomycetes")
下载树：
downloaded.tree <- tol_induced_subtree(ott_ids = taxonomy$ott_id, label_format = "name")
计算分支长度：
computed_brlen_tree <-compute.brlen(downloaded.tree)
当 plot(computed_brlen_tree) 我注意到没有单个外群时，这是为什么呢？
我需要扎根树，所以我尝试了这个：
rooted_tree = root(computed_brlen_tree, outgroup = "Russula_foetens", resolve.root = TRUE)
它改变了树的外观，我收到了这个确认：
Phylogenetic tree with 109 tips and 57 internal nodes.
Tip labels:
Rhodocollybia_butyracea, Rhodocollybia_maculata, Gymnopus_confluens, Gymnopus_peronatus, Gymnopus_dryophilus, Gymnopus_androsaceus, ...
Node labels:
Root, mrcaott109ott2361, mrcaott109ott1939, mrcaott109ott471, mrcaott109ott206, mrcaott109ott2427, ...
Rooted; includes branch lengths.
然而：
> is.rooted(computed_brlen_tree)
[1] FALSE
树还没有生根。在这种情况下指定外群的最佳方法是什么？我只是使用了出现在无根树图底部的那个。非常感谢这里的任何帮助，我是初学者，所以我可能会遗漏明显的东西。