Aim The nestedness temperature of presence–absence matrices is currently calculated with the nestedness temperature calculator (NTC). In the algorithm implemented by the NTC: (1) the line of perfect order is not uniquely defined, (2) rows and columns are reordered in such a way that the packed matrix is not the one with the lowest temperature, and (3) the null model used to determine the probabilities of finding random matrices with the same or lower temperature is not adequate for most applications. We develop a new algorithm, BINMATNEST (binary matrix nestedness temperature calculator), that overcomes these difficulties.
Methods BINMATNEST implements a line of perfect order that is uniquely defined, uses genetic algorithms to determine the reordering of rows and columns that leads to minimum matrix temperature, and provides three alternative null models to calculate the statistical significance of matrix temperature.
Results The NTC performs poorly when the input matrix has checkerboard patterns. The more efficient packing of BINMATNEST translates into matrix temperatures that are lower than those computed with the NTC. The null model implemented in the NTC is associated with a large frequency of type I error, while the other null models implemented in BINMATNEST (null models 2 and 3) are conservative. Overall, null model 3 provides the best performance. The nestedness temperature of a matrix is affected by its size and fill, but the probability that such a temperature is obtained by chance is not. BINMATNEST reorders the input matrix in such a way that, if fragment size/isolation plays a role in determining community structure, there will be a significant rank correlation between the size/isolation of the fragments and the way that they are ordered in the packed matrix.
Main conclusions The nestedness temperature of presence–absence matrices should not be calculated with the NTC. The algorithm implemented by BINMATNEST is more robust, allowing for across-study comparisons of the extent to which the nestedness of communities departs from randomness. The sequence in which BINMATNEST reorders habitat fragments provides information about the causal role of immigration and extinction in shaping the community under study.
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