README.md

tracerer

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DOI

tracerer, 'Tracer for R' is an R package to work with BEAST2 output files.

tracerer logo

tracerer is part of the babette package suite:

Related R packages:

Example

library(tracerer)

# Obtain an example log file its name
filename <- get_tracerer_path("beast2_example_output.log")

# Parse that log file
beast_log_full <- parse_beast_log(filename)

# Remove the burn-in
beast_log <- remove_burn_ins(
  beast_log_full,
  burn_in_fraction = 0.1
)

# Calculates the effective sample sizes of all parameter estimates
esses <- calc_esses(beast_log, sample_interval = 1000)

Installation

Install tracerer in R using devtools:

devtools::install_github("ropensci/tracerer")

FAQ

See FAQ

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at 'Submitting code'

I think I have found a bug

See CONTRIBUTING, at 'Submitting bugs'

There's something else I want to say

Sure, just add an Issue. Or send an email.

External links

References

Article about babette:

FASTA files anthus_aco.fas and anthus_nd2.fas from:

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ropensci/tracerer documentation built on May 14, 2019, 8:55 p.m.