Create random boolean matrices that maintain row and column sums. This is a very common use case for null models in ecology.
The package offers the newest and most efficient unbiased algorithms for generating
random matrices. Legacy approaches have used different forms of swapping, or some
alternative approaches like the
quasiswap algorithm in R's vegan package. These
methods are neither efficient, nor are they guaranteed to sample the possible
distribution of boolean vectors with a given row and column sum equally.
Currently, the package only offers an implementation of the
of Strona et al. (2014). There are two forms: a
that will randomize a sparse boolean
Matrix in-place, and a generator form:
using SparseArrays, RandomBooleanMatrices # in-place m = sprand(Bool, 1000, 1000, 0.1) randomize_matrix!(m) # using a Matrix generator object m = sprand(Bool, 1000, 1000, 0.1) rmg = matrixrandomizer(m) m1 = rand(rmg) # creates a new random matrix m2 = rand(rmg) # You can also avoid copying by m3 = rand!(rmg) # but notice that this will not create a new copy of the Matrix, so generating multiple matrices at once with this is impossible
Strona, G., Nappo, D., Boccacci, F., Fattorini, S. & San-Miguel-Ayanz, J. (2014) A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals. Nature Communications, 5, 4114.
7 months ago