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

Description

Reads a data table containing compositional data (e.g. chemical concentrations) for multiple grains and multiple samples

read.varietal(
  fname,
  snames = NULL,
  sep = ",",
  dec = ".",
  method = "KS",
  check.names = FALSE,
  row.names = 1,
  ...
)

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

x: a compositional data table

snames: a vector of strings corresponding to the sample names

name: the name of the dataset, extracted from the file path

fname: file name (character string)
snames: either a vector of sample names, an integer marking the length of the sample name prefix, or NULL. read.varietal assumes that the row names of the .csv file consist of character strings marking the sample names, followed by a number.
sep: the field separator character. Values on each line of the file are separated by this character.
dec: the character used in the file for decimal points.
method: an optional string specifying the dissimilarity measure which should be used for comparing this with other datasets. Should be one of either "KS" (for Kolmogorov-Smirnov) or "Kuiper" (for Kuiper)
check.names: logical. If TRUE then the names of the variables in the frame are checked to ensure that they are syntactically variable names.
row.names: logical. See the documentation for the read.table function.
...: optional arguments to the built-in read.csv function

fn <- system.file("SNSM/Ttn_chem.csv",package="provenance")
Ttn <- read.varietal(fname=fn,snames=3)
plot(MDS(Ttn))

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