https://github.com/walterxie/tracer
Simplified Tracer in R and Extras
https://github.com/walterxie/tracer
r-package
Last synced: about 2 months ago
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Simplified Tracer in R and Extras
- Host: GitHub
- URL: https://github.com/walterxie/tracer
- Owner: walterxie
- License: gpl-3.0
- Created: 2016-05-20T03:44:07.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2024-11-27T02:08:03.000Z (6 months ago)
- Last Synced: 2025-03-29T04:11:20.786Z (2 months ago)
- Topics: r-package
- Language: Jupyter Notebook
- Homepage:
- Size: 88.6 MB
- Stars: 9
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: COPYING
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README
# Simplified Tracer in R and Extras
In development.
## Not only the subset, but also more
This package is initially developed as a simplified implementation
of [Tracer v1.7](http://beast.community/tracer) in R.
It can take an advantage of ggplot2 to create high quality images,
and also make batch processing of multiple logs easier.
Through the development, it is growing to a package not only used as
a simple version of Tracer,
but also aiming to provide more post-analysis methods to understand
the posterior distributions from the Bayesian phylogenetic inference using MCMC.
In addition, coverage tests for a model validation are recently added.
1. For example, `readState` can extract the summary of operator proposals from
[BEAST 2](http://www.beast2.org) `*.state` log file.
```
readState("data/star.beast.state")
```
2. Summarising tree statistics from the posterior trees logged by BEAST 2,
such as the total branch length, tree height, etc.
```
tre.sta.df <- readTrees("data/RSV2long.trees")
tre.sta <- analyseTreeStats(tre.sta.df)
```
3. The [5-step pipeline](examples/Pipeline.md) to summarise the coverage tests
for validating Bayesian phylogenetic models.
## Citations
1. For Tracer, please cite:
Rambaut A, Drummond AJ, Xie D, Baele G and Suchard MA (2018),
Posterior summarisation in Bayesian phylogenetics using Tracer 1.7,
Systematic Biology. syy032.
[doi:10.1093/sysbio/syy032](https://doi.org/10.1093/sysbio/syy032)
2. For the coverage-test pipeline, please cite:
Drummond AJ, Xie D, Mendes F (),
LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses,
in preparation.
## Installation
You can use the **devtools** *install\_github()* function to install
the latest development version directly from the GitHub.
```R
library("devtools")
remove.packages("TraceR")
devtools::install_github("walterxie/TraceR")
library("TraceR")
```
Or install from `TraceR_*.tar.gz`.
```R
setwd("~/WorkSpace/TraceR")
install.packages("TraceR_?.?.?.tar.gz", repos = NULL, type = "source")
library("TraceR")
```
To see all exported functions:
```R
help(package = "TraceR")
```
Try the following commands:
```
# read MCMC log
mcmc.log <- readMCMCLog("data/star.beast.log")
# get traces and remove burn in
traces <- getTraces(mcmc.log, burn.in=0.1)
# get stats
stats <- analyseTraces(traces)
```
Please note: you can use ggplot2 instead of [gg1L](https://github.com/walterxie/gg1L)
package for visualisation.
`gtTraces(...)` is the only function depending on gg1L,
and the gg1L code will be removed from the future dependecy,
after it is replaced by the ggplot2 code.
```R
devtools::install_github("walterxie/gg1L")
library("gg1L")
```
## Tutorial (TODO update is required)