Registered S3 method overwritten by 'treeio': method from root.phylo ape ggtree v2.0.4 For help: https://yulab-smu.github.io/treedata-book/ If you use ggtree in published research, please cite the most appropriate paper(s): - Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194 - Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628 Attaching package: ‘ggtree’ The following object is masked from ‘package:ape’: rotate Warning messages: 1: In FUN(X[[i]], ...) : NAs introduced by coercion 2: In FUN(X[[i]], ...) : NAs introduced by coercion