provenance (version 0.2)

read.HMdata: Read a .csv file with categorical data

Description

Reads a data table containing categorical data (e.g. petrographic, heavy mineral or geochemical data)

Usage

read.HMdata(fname, metric = NULL)

Arguments

fname

a string with the path to the .csv file

metric

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.

Value

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

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

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

Examples

fname <- system.file("Major.csv",package="provenance")
Major <- read.HMdata(fname)
plot(getPCA(Major))