geometricMean: Geometric mean

Description Usage Arguments Details Value Note See Also Examples

Description

The geometric mean is the nth root of n products or e to the mean log of x.

Usage

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geometricMean(object, ...)

## S4 method for signature 'numeric'
geometricMean(object, removeNA = TRUE, zeroPropagate = FALSE)

## S4 method for signature 'matrix'
geometricMean(object, MARGIN = 2L)

## S4 method for signature 'sparseMatrix'
geometricMean(object, MARGIN = 2L)

Arguments

object

Object.

removeNA

logical(1). Remove NA values from calculations.

zeroPropagate

logical(1). Allow propagation of zeroes.

MARGIN

a vector giving the subscripts which the function will be applied over. E.g., for a matrix 1 indicates rows, 2 indicates columns, c(1, 2) indicates rows and columns. Where X has named dimnames, it can be a character vector selecting dimension names.

...

Additional arguments.

Details

Useful for describing non-normal (i.e. geometric) distributions.

Value

numeric.

Note

This function should be fully zero- and NA-tolerant. This calculation is not particularly useful if there are elements that are <= 0 and will return NaN.

Updated 2019-07-28.

See Also

Examples

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## numeric ====
vec1 <- seq(1L, 5L, 1L)
print(vec1)
geometricMean(vec1)

vec2 <- vec1 ^ 2L
print(vec2)
geometricMean(vec2)

## matrix ====
matrix <- matrix(
    data = c(vec1, vec2),
    ncol = 2L,
    byrow = FALSE
)
print(matrix)
geometricMean(matrix)

## sparseMatrix ====
sparse <- as(matrix, "sparseMatrix")
print(sparse)
geometricMean(sparse)

acidgenomics/basejump documentation built on Nov. 21, 2019, 1:36 a.m.