geomMean: Take the geometric mean of a vector

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

geomMean will calculate the geometric mean of a list of numerical values.

Usage

geomMean(x, rm.invalid = TRUE, default = 1e-05)

Arguments

x	A vector of numerical .
rm.invalid	Boolean value for handling 0, negative, or NA values in the vector. Default is TRUE and will not include these values in the calculation. If FALSE, these values will be replaced by the value give to default and will be included in the calculation.
default	Numerical value that serves as the value to replace 0, negative, or NA values in the calculation when rm.invalid is FALSE. Default is 1e-5.

Details

This function is a special version of the geometric mean specifically for AnaCoda. Most models in Anacoda assume a log normal distribution for phi values, thus all values in x are expectd to be positive. geomMean returns the geometric mean of a vector and can handle 0, negative, or NA values.

Value

Returns the geometric mean of a vector.

Examples

x <- c(1, 2, 3, 4)
geomMean(x)

y<- c(1, NA, 3, 4, 0, -1)
# Only take the mean of non-Na values greater than 0
geomMean(y)

# Replace values <= 0 or NAs with a default value 0.001 and then take the mean
geomMean(y, rm.invalid = FALSE, default = 0.001)

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.