trans_norm: Normalizing the nematode abundance table

In easynem: Nematode Community Analysis

Normalizing the nematode abundance table

Description

The trans_norm() is an extension of the decostand function of the vegan package for easynem-class data, which is used to standardize the nematode abundance table to reduce the order of magnitude differences of nematodes in each treatment.

Usage

trans_norm(data, method, MARGIN = 2, ...)

Arguments

data	An easynem-class data.
method	Standardization method. For details, refer to the decostand function of the vegan package.
MARGIN	Margin, 1 = rows, and 2 = columns of easynem's tab. Default MARGIN = 2.
...	Other parameters of the decostand function of the vegan package.

Details

To facilitate code interpretation, it is recommended to use the pipe symbol |> to connect functions:

nem_trans <- nem |> trans_norm(method = total)

Value

A normalized easynem-class data.

See Also

Other functions in this package for filtering and transforming data sets: filter_name, trans_formula, trans_formula_v, trans_name, filter_num, trans_rare, trans_combine

Examples

nem <- read_nem2(tab = nemtab, tax = nemtax, meta = nemmeta)
nem_trans <- nem |> trans_norm(method = total)
colSums(nem_trans@tab[,-1])
nem_trans <- nem |> trans_norm(method = percent)
colSums(nem_trans@tab[,-1])

easynem documentation built on Nov. 5, 2025, 7:39 p.m.