Package: tracerer 2.2.4

Richèl J.C. Bilderbeek

tracerer: Tracer from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev], Roberto Villegas-Diaz [ctb], David Winter [rev]

tracerer_2.2.4.tar.gz
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tracerer_2.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tracerer/json (API)

# Install 'tracerer' in R:

install.packages('tracerer', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/tracerer/issues

Pkgdown/docs site:https://docs.ropensci.org

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

7.56 score 8 stars 3 packages 85 scripts 360 downloads 1 mentions 31 exports 2 dependencies

Last updated from:31e3e09dd9 (on main). Checks:14 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	145
linux-devel-x86_64	OK	138
pkgdown docs	OK	167
source / vignettes	OK	181
linux-release-arm64	OK	154
linux-release-x86_64	OK	134
macos-release-arm64	OK	147
macos-release-x86_64	OK	214
macos-oldrel-arm64	OK	129
macos-oldrel-x86_64	OK	217
windows-devel	OK	127
windows-release	OK	89
windows-oldrel	OK	104
wasm-release	OK	140

Exports:calc_act calc_act_r calc_ess calc_esses calc_geom_mean calc_hpd_interval calc_mode calc_stderr_mean calc_summary_stats calc_summary_stats_trace calc_summary_stats_traces check_trace count_trees_in_file cs_std_dev extract_operators_lines get_tracerer_path get_tracerer_paths get_tracerer_tempfilename is_posterior is_trees_file is_trees_posterior parse_beast_log parse_beast_output_files parse_beast_posterior parse_beast_state_operators parse_beast_tracelog_file parse_beast_trees remove_burn_in remove_burn_ins save_beast_estimates save_beast_trees

Dependencies:jsonlite Rcpp

tracerer versus Tracer demo

Rendered fromdemo.Rmdusingknitr::rmarkdown

Last update: 2021-05-14
Started: 2018-02-01

Help page	Topics
Calculate the auto-correlation time, alternative implementation	calc_act
Calculate the auto correlation time from <https://github.com/beast-dev/beast-mcmc/blob/800817772033c13061f026226e41128d21fd14f3/src/dr/inference/trace/TraceCorrelation.java#L159> # nolint	calc_act_cpp
Calculate the auto-correlation time using only R. Consider using calc_act instead, as it is orders of magnitude faster	calc_act_r
Calculates the Effective Sample Size	calc_ess
Calculates the Effective Sample Sizes from a parsed BEAST2 log file	calc_esses
Calculate the geometric mean	calc_geom_mean
Calculate the Highest Probability Density of an MCMC trace that has its burn-in removed	calc_hpd_interval
Calculate the mode of values If the distribution is bi or multimodal or uniform, NA is returned	calc_mode
Calculates the standard error of the mean	calc_std_error_of_mean_cpp
Calculate the standard error of the mean	calc_stderr_mean
Calculates the Effective Sample Sizes of one estimated variable's trace	calc_summary_stats
Calculates the Effective Sample Sizes of one estimated variable's trace	calc_summary_stats_trace
Calculates the Effective Sample Sizes of the traces of multiple estimated variables	calc_summary_stats_traces
Check if the trace is a valid. Will stop if not	check_trace
Count the number of trees in a '.trees' file	count_trees_in_file
Calculate the corrected sample standard deviation	cs_std_dev
Documentation of general function arguments	default_params_doc
Extract the JSON lines out of a '.xml.state' with the unparsed BEAST2 MCMC operator acceptances file with the operators	extract_operators_lines
Get the full path of a file in the 'inst/extdata' folder	get_tracerer_path
Get the full paths of files in the 'inst/extdata' folder	get_tracerer_paths
Get a temporary filename	get_tracerer_tempfilename
Determines if the input is a BEAST2 posterior	is_posterior
Measure if a file a valid BEAST2 '.trees' file	is_trees_file
Determines if the input is a BEAST2 posterior, as parsed by parse_beast_trees	is_trees_posterior
Deprecated function to parse a BEAST2 '.log' output file. Use parse_beast_tracelog_file instead	parse_beast_log
Parse all BEAST2 output files	parse_beast_output_files
Parses BEAST2 output files to a posterior	parse_beast_posterior
Parses a BEAST2 state '.xml.state' output file to get only the operators acceptances	parse_beast_state_operators
Parses a BEAST2 tracelog '.log' output file	parse_beast_tracelog_file
Parses a BEAST2 .trees output file	parse_beast_trees
Removed the burn-in from a trace	remove_burn_in
Removed the burn-ins from a data frame	remove_burn_ins
Save the BEAST2 estimates as a BEAST2 '.log' file There will be some differences: a BEAST2 '.log' file also saves the model as comments and formats the numbers in a way non-standard to R	save_beast_estimates
Save the BEAST2 trees as a BEAST2 '.log' file There will be some differences: a BEAST2 '.log' file also saves the model as comments and formats the numbers in a way non-standard to R	save_beast_trees

Package: tracerer 2.2.4

tracerer: Tracer from R

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