Reads a data table containing compositional data (e.g. chemical concentrations)
read.compositional(
fname,
method = NULL,
colmap = "rainbow",
sep = ",",
dec = ".",
row.names = 1,
header = TRUE,
check.names = FALSE,
...
)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
name: the name of the data object, extracted from the file path
a string with the path to the .csv file
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.
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.
the field separator character. Values on each line of the file are separated by this character.
the character used in the file for decimal points.
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.
a logical value indicating whether the file contains the names of the variables as its first line.
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
fname <- system.file("Namib/Major.csv",package="provenance")
Major <- read.compositional(fname)
plot(PCA(Major))
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