An S4 class to represent compositional data.
Slots
totalsA
numericvector to store the absolute row sums (before the closure of the compositions).
Note
This class inherits from NumericMatrix.
Coerce
In the code snippets below, x is a CompositionMatrix object.
as.data.frame(x)Coerces to a
data.frame.
Subset
In the code snippets below, x is a CompositionMatrix object.
x[i, j]Extract parts of a matrix (see
[).
Examples
## Data from Aitchison 1986
data("hongite")
## Coerce to compositional data
coda <- as_composition(hongite)
## codaccess
dim(coda) # Get the matrix dimensions
#> [1] 25 5
row(coda) # Get the row indexes
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 2 2 2 2 2
#> [3,] 3 3 3 3 3
#> [4,] 4 4 4 4 4
#> [5,] 5 5 5 5 5
#> [6,] 6 6 6 6 6
#> [7,] 7 7 7 7 7
#> [8,] 8 8 8 8 8
#> [9,] 9 9 9 9 9
#> [10,] 10 10 10 10 10
#> [11,] 11 11 11 11 11
#> [12,] 12 12 12 12 12
#> [13,] 13 13 13 13 13
#> [14,] 14 14 14 14 14
#> [15,] 15 15 15 15 15
#> [16,] 16 16 16 16 16
#> [17,] 17 17 17 17 17
#> [18,] 18 18 18 18 18
#> [19,] 19 19 19 19 19
#> [20,] 20 20 20 20 20
#> [21,] 21 21 21 21 21
#> [22,] 22 22 22 22 22
#> [23,] 23 23 23 23 23
#> [24,] 24 24 24 24 24
#> [25,] 25 25 25 25 25
col(coda, as.factor = TRUE) # Get the column indexes
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] A B C D E
#> [2,] A B C D E
#> [3,] A B C D E
#> [4,] A B C D E
#> [5,] A B C D E
#> [6,] A B C D E
#> [7,] A B C D E
#> [8,] A B C D E
#> [9,] A B C D E
#> [10,] A B C D E
#> [11,] A B C D E
#> [12,] A B C D E
#> [13,] A B C D E
#> [14,] A B C D E
#> [15,] A B C D E
#> [16,] A B C D E
#> [17,] A B C D E
#> [18,] A B C D E
#> [19,] A B C D E
#> [20,] A B C D E
#> [21,] A B C D E
#> [22,] A B C D E
#> [23,] A B C D E
#> [24,] A B C D E
#> [25,] A B C D E
#> Levels: A B C D E
nrow(coda) # Get the number of rows
#> [1] 25
ncol(coda) # Get the number of columns
#> [1] 5
dimnames(coda) # Get the dimension names
#> [[1]]
#> [1] "H1" "H2" "H3" "H4" "H5" "H6" "H7" "H8" "H9" "H10" "H11" "H12"
#> [13] "H13" "H14" "H15" "H16" "H17" "H18" "H19" "H20" "H21" "H22" "H23" "H24"
#> [25] "H25"
#>
#> [[2]]
#> [1] "A" "B" "C" "D" "E"
#>
rownames(coda) <- LETTERS[1:25] # Set the row names
rownames(coda) # Get the rownames
#> [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S"
#> [20] "T" "U" "V" "W" "X" "Y"
colnames(coda) <- letters[21:25] # Set the column names
colnames(coda) # Get the column names
#> [1] "u" "v" "w" "x" "y"