An S4 class to represent compositional data.
Note
This class inherits from matrix.
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
[).
See also
Other classes:
LogRatio-class,
LogicalMatrix-class,
NumericMatrix-class,
OutlierIndex-class
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"