collapse_by_taxonomy: Collapse by taxonomy

In surh/AMOR: Abundance Matrix Operations in R

Collapse by taxonomy

Description

Collapses taxa according to the taxonomy object or a given factor

Usage

collapse_by_taxonomy(...)

## Default S3 method:
collapse_by_taxonomy(
  Tab,
  Tax,
  Group = NULL,
  level = 4,
  FUN = sum,
  sepchar = ";"
)

## S3 method for class 'Dataset'
collapse_by_taxonomy(Dat, Group = NULL, level = 4, FUN = sum, sepchar = ";")

Arguments

Tab	An abundance matrix with samples as columns and taxa as rows
Tax	A Taxonomy data.frame as defined by create_dataset
Group	If NULL, then the "Taxonomy" column of the Taxonomy data.frame will be used. If not NULL, it can be either a column number or name (i.e. character string), indicating which column of the Taxonomy data.frame to use as grouping factor. It can also be a factor or vector that can be coerced into factor.
level	If Group is NULL, the taxonomy level to use from the Taxonomy column.
FUN	Which function to use to aggregate
sepchar	Separator character for taxonomy levels.

Value

The default method returns a numeric matrix.

The Dataset method returns a Dataset object when Dat includes a Map element (see create_dataset). When the Map element is missing it returns a matrix object.

Author(s)

Sur Herrera Paredes

See Also

create_dataset

Examples

library(AMOR)
data(Rhizo)
data(Rhizo.map)
data(Rhizo.tax)

Dat <- create_dataset(Tab = Rhizo, Map = Rhizo.map, Tax = Rhizo.tax)
Dat.phyl <- collapse_by_taxonomy(Dat = Dat, level = 4)

# The followwing returns a matrix
Dat.collapsed1 <- collapse_by_taxonomy(Dat$Tab, Dat$Tax)

# The following returns a dataset object
Dat.collapsed2 <- collapse_by_taxonomy(Dat=Dat)

surh/AMOR documentation built on Feb. 21, 2023, 6:31 a.m.