prop_abund: prop_abund

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

prop_abund

Description

Calculates proportional abundance of each species (columns) across samples (rows) in community data matrix m. Row sums of output matrix will all be 1.

Usage

prop_abund(
  m,
  to_int = FALSE,
  max_int = floor(sqrt(.Machine$integer.max)),
  speciesRows = FALSE
)

Arguments

m	matrix or data frame of numeric values. Columns represent species, rows are samples.
to_int	logical. Should output matrix be transformed into integers from 0 to max_int? Integers take up half as much space as doubles, and as weights are equivalent for calculating specificity. The tradeoff is a little bit of precision (default: FALSE).
max_int	integer. Maximum integer value used for to_int. If pairwise geometric means will be calculated with these data, it is nice to keep this value as the square root of the maximum integer size, which is the default.
speciesRows	logical. Do rows represent species (instead of samples)? (default:FALSE)

Value

matrix of proportional abundances.

Author(s)

John L. Darcy

Examples

# library(specificity)
# attach(endophyte)
# m_dbl <- prop_abund(otutable)
# m_int <- prop_abund(otutable, to_int=TRUE)
# head(rowSums(m_dbl))
# head(rowSums(m_int))
# # note that they are off by a little bit. This small loss in precision is OK.
# object.size(m_dbl)
# object.size(m_int)
# random_positions <- random_rep_positions(m_dbl, 100)
# plot(m_int[random_positions] ~ m_dbl[random_positions])

darcyj/specificity documentation built on Aug. 1, 2023, 8 a.m.