summarizeTrace: Summarize trace

In RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Summarize trace

Description

Summarizes trace file(s) that have been read into memory

Usage

summarizeTrace(trace, vars)

Arguments

trace	(list of data frames; no default) Name of a list of data frames, such as produced by readTrace(). If the readTrace() output contains multiple traces (such as from multiple runs), summarizeTrace() will provide summaries for each trace individually, as well as the combined trace.
vars	(character or character vector; no default) The name of the variable(s) to be summarized.

Details

Summarizes a trace file for continuous or discrete characters by computing the mean and 95% credible interval for quantitative character and the 95% credible set for discrete characters.

Value

summarizeTrace() returns a list of the length of provided variables. For quantitative variables, it returns the mean and 95 For discrete variables, it returns the 95 associated probabilities.

Examples

# continuous character only example, one run

# download the example dataset to working directory
url_gtr <-
    "https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR.log"
dest_path_gtr <- "primates_cytb_GTR.log"
download.file(url_gtr, dest_path_gtr)

# to run on your own data, change this to the path to your data file
file_single <- dest_path_gtr

one_trace <- readTrace(paths = file_single)
trace_sum <- summarizeTrace(trace = one_trace,
                            vars = c("pi[1]","pi[2]","pi[3]","pi[4]"))
trace_sum[["pi[1]"]]

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_gtr)

# continuous character example, multiple runs

#' # download the example dataset to working directory
url_1 <-
"https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR_run_1.log"
dest_path_1 <- "primates_cytb_GTR_run_1.log"
download.file(url_1, dest_path_1)

url_2 <-
"https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR_run_2.log"
dest_path_2 <- "primates_cytb_GTR_run_2.log"
download.file(url_2, dest_path_2)

# to run on your own data, change this to the path to your data file
file_1 <- dest_path_1
file_2 <- dest_path_2

# read in the multiple trace files
multi_trace <- readTrace(path = c(file_1, file_2), burnin = 0.0)

trace_sum_multi <- summarizeTrace(trace = multi_trace,
                                  vars = c("pi[1]","pi[2]","pi[3]","pi[4]"))
trace_sum_multi[["pi[1]"]]

# remove files
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_1, dest_path_2)

# discrete character example

# download the example dataset to working directory
url_rj <- "https://revbayes.github.io/tutorials/intro/data/freeK_RJ.log"
dest_path_rj <- "freeK_RJ.log"
download.file(url_rj, dest_path_rj)

file <- dest_path_rj
trace <- readTrace(path = file)

trace_sum_discrete <- summarizeTrace(trace = trace,
                                     vars = c("prob_rate_12",
                                              "prob_rate_13",
                                              "prob_rate_31",
                                              "prob_rate_32"))
trace_sum_discrete[["prob_rate_12"]]

#' # remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_rj)

RevGadgets documentation built on May 29, 2024, 10:03 a.m.