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Background:  Taxa Indicator Threshold ANalysis (TITAN) was developed to identify thresholds along environmental gradients where rapid changes in taxa frequency and relative abundance are observed. TITAN determines separate change-points for increasing and decreasing taxa in aggregate, as well as change-points for individual taxa, with associated confidence intervals generated using bootstrapping. However, if TITAN is applied to different classes of observations, additional analyses besides using non-overlapping confidence intervals are needed to establish whether change-points differ between treatments or groups because non-overlapping confidence intervals can indicate significant differences but overlapping confidence intervals do not necessarily mean the null hypothesis cannot be rejected.    Methods:  To address this, we present a new R package, pTITAN2, which is an extension to the existing TITAN2 package. The pTITAN2 package was developed to enable comparisons of TITAN output between treatments by permutating the observed data between treatments and rerunning TITAN on the permuted data.    Results:  The pTITAN2 package includes two functions, occurrences and permute. The occurrences function selects the taxonomic codes to be used in a TITAN run while maintaining the most taxonomic details. The permute function is then used to create a list of permuted sets of taxa and environmental gradients. TITAN is then run again on the permuted data and p-value test can be calculated using the observed and permuted TITAN output to test for statistical differences between treatment effects.    Conclusions:  The package pTITAN2 is an extension of the existing TITAN2 package and enables users to perform the appropriate statistical tests and determine statistical differences without using overlapping confidence intervals.

pTITAN2: Permutation of treatment labels and Threshold Indicator Taxa ANalysis