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No "read.r8s" #619

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WXwangxia opened this issue Jun 20, 2024 · 2 comments
Open

No "read.r8s" #619

WXwangxia opened this issue Jun 20, 2024 · 2 comments

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@WXwangxia
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dear author,
i wanna visualize the result of r8s, which is a program for analysis of rates of evolution.
Fortunately, i found the ggtree package that could realize it. but when i use it, something was wrong.
below that:

Describe my issue

setwd("C:/Users/wx/Desktop/forBEAST/beast_44digital/rename_nex")
library(ggtree)
read.r8s("44re.out")
错误于read.r8s("44re.out"): 没有"read.r8s"这个函数

Could someone tell me how to solve this problem please? i will appreciate it from the bottom of my heart!!

best wishes

@WXwangxia
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HAHAHA, i found this "read.r8s" package, though error in parsing the out file.
a little happy~~~

require(treeio)
载入需要的程序包:treeio
treeio v1.28.0 For help:
https://yulab-smu.top/treedata-book/

If you use the ggtree package suite in published research, please
cite the appropriate paper(s):

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

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
Guangchuang Yu. Data Integration, Manipulation and Visualization
of Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
doi:10.1201/9781003279242

y = read.r8s("44re.out")
错误于read.r8s("44re.out"): fail to parse the file...

@WXwangxia
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44re_output.log
Could someone please help check why the result file of r8s cannot be parsed by read.r8s? thanks very much!!!

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