getMAP: get MAP
In revbayes/RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

getMAP

R Documentation

get MAP

Description

Calculates the Maximum a Posteriori estimate for the trace of a quantitative variable

Usage

getMAP(var)

Arguments

var

(numeric vector; no default) Vector of the samples from the trace of a quantitative variable

Details

Uses the SANN method of the optim() function to approximate the MAP estimate

Value

the MAP estimate

Examples



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

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

trace <- readTrace(paths = file)
MAP <- getMAP(trace[[1]]$"pi[1]")

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

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.