Absolute Frequency Matrix

An S4 class to represent an absolute frequency matrix (i.e. the number of times a given datum occurs in a dataset).

CountMatrix(data = 0, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)

Arguments

data	an optional data vector (including a list or `expression` vector). Non-atomic classed R objects are coerced by `as.vector` and all attributes discarded.
nrow	the desired number of rows.
ncol	the desired number of columns.
byrow	logical. If `FALSE` (the default) the matrix is filled by columns, otherwise the matrix is filled by rows.
dimnames	A `dimnames` attribute for the matrix: `NULL` or a `list` of length 2 giving the row and column names respectively. An empty list is treated as `NULL`, and a list of length one as row names. The list can be named, and the list names will be used as names for the dimensions.

Author

N. Frerebeau

Examples

## Create an incidence (presence/absence) matrix
## Data will be coerced with as.logical()
A <- IncidenceMatrix(data = sample(0:1, 100, TRUE, c(1, 1/3)), nrow = 20)
## Create a count data matrix
B <- CountMatrix(data = sample(0:10, 100, TRUE), nrow = 20)

## Access
dim(B) # Get the matrix dimensions
#> [1] 20  5
row(B) # 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
col(B, as.factor = TRUE) # Get the column indexes
#>       [,1] [,2] [,3] [,4] [,5]
#>  [1,] col1 col2 col3 col4 col5
#>  [2,] col1 col2 col3 col4 col5
#>  [3,] col1 col2 col3 col4 col5
#>  [4,] col1 col2 col3 col4 col5
#>  [5,] col1 col2 col3 col4 col5
#>  [6,] col1 col2 col3 col4 col5
#>  [7,] col1 col2 col3 col4 col5
#>  [8,] col1 col2 col3 col4 col5
#>  [9,] col1 col2 col3 col4 col5
#> [10,] col1 col2 col3 col4 col5
#> [11,] col1 col2 col3 col4 col5
#> [12,] col1 col2 col3 col4 col5
#> [13,] col1 col2 col3 col4 col5
#> [14,] col1 col2 col3 col4 col5
#> [15,] col1 col2 col3 col4 col5
#> [16,] col1 col2 col3 col4 col5
#> [17,] col1 col2 col3 col4 col5
#> [18,] col1 col2 col3 col4 col5
#> [19,] col1 col2 col3 col4 col5
#> [20,] col1 col2 col3 col4 col5
#> Levels: col1 col2 col3 col4 col5
nrow(B) # Get the number of rows
#> [1] 20
ncol(B) # Get the number of columns
#> [1] 5
dimnames(B) # Get the dimension names
#> [[1]]
#>  [1] "row1"  "row2"  "row3"  "row4"  "row5"  "row6"  "row7"  "row8"  "row9" 
#> [10] "row10" "row11" "row12" "row13" "row14" "row15" "row16" "row17" "row18"
#> [19] "row19" "row20"
#> 
#> [[2]]
#> [1] "col1" "col2" "col3" "col4" "col5"
#> 
rownames(B) <- LETTERS[1:20] # Set the row names
rownames(B) # 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"
colnames(B) <- letters[21:25] # Set the column names
colnames(B) # Get the column names
#> [1] "u" "v" "w" "x" "y"

## Subset
B[[1, 1]] # Get the first value
#> [1] 1
B[1] # Get the first value
#> [1] 1
B[, ] # Get all values
#> <CountMatrix: 20 x 5>
#>    u  v  w  x y
#> A  1  6 10  6 9
#> B  6  3  1 10 1
#> C  2  3  9  9 8
#> D  9  3 10  6 9
#> E  7  2  7  5 5
#> F  2  4  1  4 9
#> G  0  5  5  9 1
#> H  0  4  5  8 1
#> I  8  2  0  5 8
#> J  9  3  4  7 0
#> K  9  8  4  2 0
#> L 10  4  5  9 0
#> M  4  5  8  9 0
#> N  1  6  0 10 8
#> O  9  6  0  1 1
#> P 10  9  8  9 2
#> Q  7  5  3  6 8
#> R  1  4  1  6 4
#> S  3  7  7  3 7
#> T  4 10  6  6 5
B[1, , drop = FALSE] # Get the first row
#> <CountMatrix: 1 x 5>
#>   u v  w x y
#> A 1 6 10 6 9
B[, 1:3] # Get the first three column
#> <CountMatrix: 20 x 3>
#>    u  v  w
#> A  1  6 10
#> B  6  3  1
#> C  2  3  9
#> D  9  3 10
#> E  7  2  7
#> F  2  4  1
#> G  0  5  5
#> H  0  4  5
#> I  8  2  0
#> J  9  3  4
#> K  9  8  4
#> L 10  4  5
#> M  4  5  8
#> N  1  6  0
#> O  9  6  0
#> P 10  9  8
#> Q  7  5  3
#> R  1  4  1
#> S  3  7  7
#> T  4 10  6

Arguments

See also

Author

Examples