occasional_occupancy: Excludes occasional species defined by occupancy

In fsfrazao/SharedS: Assessing the influence of occasional species on shared-species metrics

Description

This function considers any species with total occupancy lower than the specified occupancy class to be an occasional species. It replaces the abundance of occasional species with zeros.

Usage

occasional_occupancy(data, occup_class, abund_class = 0,
  dont_apply_to = 0)

Arguments

data	A data.frame containing species in the columns and samples in the rows.
occup_class	The occupancy threshold. Species for which the total occupancy is lower than this value are considered occasional. The function considers the total occupancy (i.e.: the number of samples/rows in which the species is present).
abund_class	The abundance threshold.If greater than zero, applies the occasional_abundance function before excluding by occupancy. Species for which the total abundance is lower than this value are considered occasional. The total abundance (i.e.: the sum accross all samples/rows) not the abundance per sample.
dont_apply_to	A list of species (as column names or indices) to disregard. These species abundances will not be modified even if their total abundances are below the abund_class threshold.

Value

The community data with occasional species replaced by zeros

Examples

data(community_data)

#Select all samples in Evironment 'A'
comm.A<-community_data[which(community_data$environment == "A"),]

# Select only the abundance matrix (columns 1 and 2 contain the 'environment' and 'sample' data)
comm.A <- comm.A[, 3:ncol(comm.A)]

Consider all species with total occupancy lower than 3 to be occasional.
These will be replaced by zeros, such as sp.5, sp.15, sp.21 and sp.23.


occasional_occupancy(comm.A,3)
    sp1 sp2 sp3 sp4 sp5 sp6 sp7 sp8 sp9 sp10 sp11 sp12 sp13 sp14 sp15 sp16
[1,]   5   2   3   8   0   6   3  10   1    0    2    5    1    8    0    2
[2,]   1   8   6   2   0   7   6   2   3    0    1   10    9    6    0    8
[3,]   5   2   6   5   0  10   6  10   7    0    7    8   10    2    0    2
[4,]   6   2   5   6   0   7   1   5   8    0    0    3    1    6    0    1
[5,]   6   3   4   2   0   6   3   7   6    0    2    2    6   10    0    8
     sp17 sp18 sp19 sp20 sp21 sp22 sp23 sp24 sp25 sp26 sp27 sp28 sp29 sp30
[1,]    8    9    5    5    0    4    0    9    6    9    7    9    8    4
[2,]    0    7   10    3    0    2    0    3    9    7    2    8    3    7
[3,]    9    4    1   10    0   10    0    9    5    4    2    3    2    8
[4,]    4    3   10    2    0   10    0    0    9    7    6    2    6    4
[5,]    5    3    4    2    0    0    0    8    2    9   10   10    3    2

fsfrazao/SharedS documentation built on July 1, 2019, 6:24 p.m.