read.compositional: Read a .csv file with compositional data

Description Usage Arguments Value Examples

View source: R/io.R

Description

Reads a data table containing compositional data (e.g. chemical concentrations)

Usage

1
read.compositional(fname, method = NULL, colmap = "rainbow")

Arguments

fname

a string with the path to the .csv file

method

either "bray" (for the Bray-Curtis distance) or "aitchison" (for Aitchison's central logratio distance). If omitted, the function defaults to 'aitchison', unless there are zeros present in the data.

colmap

an optional string with the name of one of R's built-in colour palettes (e.g., heat.colors, terrain.colors, topo.colors, cm.colors), which are to be used for plotting the data.

Value

an object of class compositional, i.e. a list with the following items:

x: a data frame with the samples as rows and the categories as columns

method: either "aitchison" (for Aitchison's centred logratio distance) or "bray" (for the Bray-Curtis distance)

colmap: the colour map provided by the input argument

Examples

1
2
3
    fname <- system.file("Major.csv",package="provenance")
    Major <- read.compositional(fname)
    plot(PCA(Major))

provenance documentation built on April 24, 2018, 5:04 p.m.