These functions convert a community data to compressed sparse matrix, dense matrix and long format (e.g. species records).
long2sparse(x, grids = "grids", species = "species")
sparse2long(x)
dense2sparse(x)
sparse2dense(x)
long2dense(x)
dense2long(x)A community data which one wants to transform
column name of the column containing grid cells
column name of the column containing the species / taxa names
A compressed sparse community matrix of sites by species
data(africa)
africa$comm[1:5, 1:20]
#> 5 x 20 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 20 column names ‘Abutilon_angulatum_OM1934’, ‘Abutilon_sonneratianum_LTM034’, ‘Acalypha_chirindica_OM2341’ ... ]]
#>
#> v3635 . . . . . . . . . 1 . . . . . . . . . .
#> v3636 . . . . . . . . . 1 . . . . . . . . . 1
#> v3637 . . . . . . . . . 1 . . . . . . . . . 1
#> v3638 . . . . . . . . . 1 . . . . . . . . . .
#> v3639 . . . . . . . . . 1 . . . . . . . . . .
long <- sparse2long(africa$comm)
long[1:5, ]
#> grids species
#> 1 v3757 Abutilon_angulatum_OM1934
#> 2 v3758 Abutilon_angulatum_OM1934
#> 3 v3759 Abutilon_angulatum_OM1934
#> 4 v3826 Abutilon_angulatum_OM1934
#> 5 v3827 Abutilon_angulatum_OM1934
sparse <- long2sparse(long)
all.equal(africa$comm, sparse)
#> [1] "Component “Dimnames”: Component 2: 10 string mismatches"
#> [2] "Mean relative difference: 2"
dense_comm <- matrix(c(1,0,1,1,0,0,
1,0,0,1,1,0,
1,1,1,1,1,1,
0,0,1,1,0,1), 6, 4,
dimnames=list(paste0("g",1:6), paste0("sp", 1:4)))
dense_comm
#> sp1 sp2 sp3 sp4
#> g1 1 1 1 0
#> g2 0 0 1 0
#> g3 1 0 1 1
#> g4 1 1 1 1
#> g5 0 1 1 0
#> g6 0 0 1 1
sparse_comm <- dense2sparse(dense_comm)
sparse_comm
#> 6 x 4 sparse Matrix of class "dgCMatrix"
#> sp1 sp2 sp3 sp4
#> g1 1 1 1 .
#> g2 . . 1 .
#> g3 1 . 1 1
#> g4 1 1 1 1
#> g5 . 1 1 .
#> g6 . . 1 1
sparse2long(sparse_comm)
#> grids species
#> 1 g1 sp1
#> 2 g3 sp1
#> 3 g4 sp1
#> 4 g1 sp2
#> 5 g4 sp2
#> 6 g5 sp2
#> 7 g1 sp3
#> 8 g2 sp3
#> 9 g3 sp3
#> 10 g4 sp3
#> 11 g5 sp3
#> 12 g6 sp3
#> 13 g3 sp4
#> 14 g4 sp4
#> 15 g6 sp4