update read.nhx to parse large tree file

[xiangpin]

Description

• original read.nhx is too slow to parse large tree file, since it has loop to replace the node labels. I used gsub to ajust the metadata to labels. e.g. "t1:0.03[&&NHX:test=1]" to "t1[&&NHX:test=1]:0.03", then the next steps are similar with processing of beast file.
• I also used gsub to ajust the metadata of beast for "t1:0.01[&test=1,rare=0.5]" to "t1[&test=1,rare=0.5]:0.01"
• adjust the type of metadata of astral tree file to numetic when it is needed.

Related Issue

• the large nhx tree file in #12
• the rd and examples of write.beast.newick and read.beast.newick in #50 was incorrect. I has adjusted them
• root.phylo has been removed in treeio since it will generate warnings. #45

  Example

  
  > library(treeio)
  treeio v1.15.5  For help: https://yulab-smu.top/treedata-book/

If you use treeio in published research, please cite:

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240

system.time(tr <- read.nhx("./test.nhx")) user system elapsed 2.016 0.016 2.044 tr 'treedata' S4 object that stored information of './test.nhx'.

...@ phylo: Phylogenetic tree with 20000 tips and 19999 internal nodes.

Tip labels: aaaaaabmnp, aaaaaabmnq, aaaaaabmnr, aaaaaabmns, aaaaaabmnt, aaaaaabmnu, ... Node labels: , NoName, NoName, NoName, NoName, NoName, ...

Rooted; no branch lengths.

with the following features available: 'dist', 'support'.

<!--- Did you remember to include tests? Unless you're just changing
grammar, please include new tests for your change -->

[GuangchuangYu]

good work :)

[brj1]

I've found that read.beast is also slow. If you want read in a beast tree file with 10,000 trees, it is basically impossible. I wonder if similar improvements could be made to read.beast.