tbea (version 1.5.0)

lognormalBeast: Constructing a curve for the user-specified lognormal prior using Beast2 parameters

Description

Constructing a curve for the user-specified lognormal prior using Beast2 parameters

Usage

lognormalBeast(
  M,
  S,
  meanInRealSpace = TRUE,
  offset = 0,
  from = NULL,
  to = NULL,
  by = 0.05
)

Value

A matrix of two columns consisting of the x and y values of the lognormal density.

Arguments

M

Mean of the lognormal density in Beast2.

S

Standard deviation of the lognormal density in Beast2.

meanInRealSpace

Whether to plot the mean on the real- or log-space (i.e., apply log(M) before plotting). Please see under details.

offset

Hard lower bound.

from, to, by

Starting and ending point to calculate considering the offset as zero. That is, from will affect produce a starting point of (offset + from) and an ending point of (offset + to). By sets the step size of the sequence from `from` to `to` each `by` steps.

Details

This function creates a matrix of x,y values given parameters of a lognormal density as specified in the program Beast2. It's main purpose is for plotting but other uses such as similarity quantification are available. Please note that the value of mean depends on whether we expect it to be in real or log space. Please refer to Heath (2015) for more info: Heath, T. A. (2015). Divergence Time Estimation using BEAST v2.

Examples

# Generate a matrix for the lognormal density with mean 1 and standard deviation 1, with mean
# in real space, and spanning values in x from 0 to 10
lognormalBeast(M = 1, S = 1, meanInRealSpace = TRUE, from = 0, to = 10)
# The same as above but with an offset of 10, that is, the curve starts at 10 as if it was 0
# to values will start in (offset + from) and finish in (offset + to)
lognormalBeast(M = 1, S = 1, meanInRealSpace = TRUE, offset = 10, from = 0, to = 10)