An S4 class to represent compositional data.
Slots
totalsA
numericvector to store the absolute row sums (before the closure of the compositions).codesA
charactervector to store the laboratory codes (unique identifiers).samplesA
charactervector to store the sample identifiers (allows duplicates in case of repeated measurements).groupsA
charactervector to store the group names (if any).
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"