read.compositional | R Documentation |
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,
...
)
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. |
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 |
... |
optional arguments to the built-in |
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
fname <- system.file("Namib/Major.csv",package="provenance")
Major <- read.compositional(fname)
plot(PCA(Major))
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