read.counts: Read a .csv file with point-counting data

Description

Reads a data table containing point-counting data (e.g. petrographic, heavy mineral, palaeontological or palynological data)

Usage

read.counts(
  fname,
  method = "chisq",
  colmap = "rainbow",
  sep = ",",
  dec = ".",
  row.names = 1,
  header = TRUE,
  check.names = FALSE,
  ...
)

Value

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

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

colmap: the colour map provided by the input argument

name: the name of the data object, extracted from the file path

Arguments

fname: a string with the path to the .csv file
method: either "chisq" (for the chi-square distance) or "bray" (for the Bray-Curtis distance)
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.
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.
row.names: a vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the which contains the row names, or character string the name of the table column containing the row names.
header: a logical value indicating whether the file contains the names of the variables as its first line.
check.names: logical. If TRUE then the names of the variables in the frame are checked to ensure that they are syntactically variable names.
...: optional arguments to the built-in read.table function

Examples

Run this code

    fname <- system.file("Namib/HM.csv",package="provenance")
    Major <- read.counts(fname)
    #plot(PCA(HM))

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