问题描述
当我尝试将小标题转换为树（treedata 或 phylo）对象时出错，即使小标题最初是由树生成的。见示例：
library(ape,quietly = TRUE,warn.conflicts = FALSE)
library(tidytree,warn.conflicts = FALSE)
library(treeio,warn.conflicts = FALSE)
#> treeio v1.14.4 For help: https://yulab-smu.top/treedata-book/
set.seed(2017)
a <- rtree(4) %>% as_tibble() %>% as.data.frame()
#> Warning: UnkNown or uninitialised column: `node`.
print(a)
#> parent node branch.length label
#> 1 5 1 0.434905600 t4
#> 2 7 2 0.674331481 t1
#> 3 7 3 0.002020766 t3
#> 4 6 4 0.025093514 t2
#> 5 5 5 NA <NA>
#> 6 5 6 0.472166386 <NA>
#> 7 6 7 0.273833123 <NA>
# ERROR ON BOTH
a %>% as.treedata() #calls treeio:::as.treedata.data.frame which calls treeio:::as.phylo.tbl_df
#> Error in check_edgelist(x): Cannot find root. network is not a tree!
a %>% as.phylo() #calls treeio:::as.phylo.data.frame which is equal to treeio:::as.phylo.tbl_df
#> Error in check_edgelist(x): Cannot find root. network is not a tree!
它要求 'unique(parents[!(parents %in% children)])' 返回一个非零向量， 但这与根节点本身的性质相反：
例如tidytree:::rootnode.tbl_tree 将根定义为具有 parent==node
的节点由 reprex package (v1.0.0) 于 2021 年 6 月 4 日创建
会话信息sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.5 (2021-03-31)
#> os Ubuntu 20.04.2 LTS
#> system x86_64,linux-gnu
#> ui X11
#> language (EN)
#> collate C.UTF-8
#> ctype C.UTF-8
#> tz Etc/UTC
#> date 2021-06-04
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
#> ape * 5.5 2021-04-25 [1] CRAN (R 4.0.5)
#> assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.4)
#> cli 2.3.1 2021-02-23 [2] CRAN (R 4.0.4)
#> Crayon 1.4.1 2021-02-08 [2] CRAN (R 4.0.4)
#> DBI 1.1.1 2021-01-15 [2] CRAN (R 4.0.4)
#> digest 0.6.27 2020-10-24 [2] CRAN (R 4.0.4)
#> dplyr 1.0.5 2021-03-05 [2] CRAN (R 4.0.4)
#> ellipsis 0.3.1 2020-05-15 [2] CRAN (R 4.0.4)
#> evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.4)
#> fansi 0.4.2 2021-01-15 [2] CRAN (R 4.0.4)
#> fs 1.5.0 2020-07-31 [2] CRAN (R 4.0.4)
#> generics 0.1.0 2020-10-31 [2] CRAN (R 4.0.4)
#> glue 1.4.2 2020-08-27 [2] CRAN (R 4.0.4)
#> highr 0.8 2019-03-20 [2] CRAN (R 4.0.4)
#> htmltools 0.5.1.1 2021-01-22 [2] CRAN (R 4.0.4)
#> jsonlite 1.7.2 2020-12-09 [2] CRAN (R 4.0.4)
#> knitr 1.31 2021-01-27 [2] CRAN (R 4.0.4)
#> lattice 0.20-41 2020-04-02 [4] CRAN (R 4.0.0)
#> lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.0.4)
#> lifecycle 1.0.0 2021-02-15 [2] CRAN (R 4.0.4)
#> magrittr 2.0.1 2020-11-17 [2] CRAN (R 4.0.4)
#> nlme 3.1-152 2021-02-04 [4] CRAN (R 4.0.3)
#> pillar 1.5.1 2021-03-05 [2] CRAN (R 4.0.4)
#> pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.0.4)
#> purrr 0.3.4 2020-04-17 [2] CRAN (R 4.0.4)
#> R6 2.5.0 2020-10-28 [2] CRAN (R 4.0.4)
#> Rcpp 1.0.6 2021-01-15 [2] CRAN (R 4.0.4)
#> reprex 1.0.0 2021-01-27 [2] CRAN (R 4.0.4)
#> rlang 0.4.10 2020-12-30 [2] CRAN (R 4.0.4)
#> rmarkdown 2.7 2021-02-19 [2] CRAN (R 4.0.4)
#> rstudioapi 0.13 2020-11-12 [2] CRAN (R 4.0.4)
#> sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 4.0.4)
#> stringi 1.5.3 2020-09-09 [2] CRAN (R 4.0.4)
#> stringr 1.4.0 2019-02-10 [2] CRAN (R 4.0.4)
#> tibble 3.1.0 2021-02-25 [2] CRAN (R 4.0.4)
#> tidyselect 1.1.0 2020-05-11 [2] CRAN (R 4.0.4)
#> tidytree * 0.3.4 2021-05-22 [1] CRAN (R 4.0.5)
#> treeio * 1.14.4 2021-04-26 [1] Bioconductor
#> utf8 1.2.1 2021-03-12 [2] CRAN (R 4.0.4)
#> vctrs 0.3.7 2021-03-29 [2] CRAN (R 4.0.4)
#> withr 2.4.1 2021-01-26 [2] CRAN (R 4.0.4)
#> xfun 0.22 2021-03-11 [2] CRAN (R 4.0.4)
#> yaml 2.2.1 2020-02-01 [2] CRAN (R 4.0.4)
#>
#> [1] /home/edoardo/R/x86_64-pc-linux-gnu-library/4.0
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
解决方法
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