read_hst: Reads ADMB hst files

In einarhjorleifsson/mriass: A collection of various functions used in stock assessment

Description

Reads output of ADMB MCMC report containing estimated distributions. The .hst report contains information about the MCMC analysis: the sample sizes (specied with the -mcmc command-line option), the step size scaling factor, the step sizes, and information about the posterior probability distribution (e.g., the mean, standard deviation, and lower and upper bounds). For each simulated parameter, a range of values (with step sizes reported in the "step sizes" section of the .hst file) and their simulated posterior probabilities is reported. Plotting the first column (parameter values) on the x-axis and the second column (simulated probabilities) on the y-axis can be a convenient way to make a visualization of the posterior probability distribution.

Usage

read_hst(file, dir, txt, startyear, names, negative.allowed = FALSE)

Arguments

file	Name of the file, normally ends with .hst
dir	Name of the directory that contains the result.
txt	The parameters to extract
startyear	Assessment start year
names	A character vector of length two replacing the default names c('value','prop')
negative.allowed	Flag, default is FALSE

Value

A list, each component being a dataframe with two columns. The default names are c('value','prop') which can be replace by specifying names.

einarhjorleifsson/mriass documentation built on May 16, 2019, 1:30 a.m.