occ_threshold: occ_threshold

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

occ_threshold

Description

removes species (columns) from a matrix that don't meet a minimum occupancy, defined as the number of samples in which that species was observed.

Usage

occ_threshold(m, threshold, max_absent = 0)

Arguments

m	matrix or data frame of numeric values. Columns represent species, rows are samples.
threshold	integer. Minimum number of samples a species can occupy without being removed.
max_absent	float. Maximum abundance value at which a species will be considered absent (default: 0).

Value

matrix with low-occupancy species removed.

Author(s)

John L. Darcy

Examples

# library(specificity)
# attach(endophyte)
# dim(otutable)
# otutable_over25 <- occ_threshold(otutable, 25)
# dim(otutable_over25)

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