pTITAN2

pTITAN2 is an extension to the TITAN2 package by Matthew E. Baker, Ryan S. King and David Kahle. The TITAN2 package is used for performing Taxa Indicator Threshold ANalysis (TITAN) in R (Baker and King, 2010). The TITAN2 package generates change points along an environmental gradient for individual taxa and for composites of increasing or decreasing taxa, along with associated confidence intervals, the latter via bootstrapping. While some scientists examine the overlap between confidence intervals to determine whether the difference between two point estimates is significantly different, this approach is more conservative than the standard approach for assessing significant differences and rejects the null hypothesis less often than standard approaches (Schenker and Gentleman 2001, Greenland et al. 2016). "As with P values, comparison between groups requires statistics that directly test and estimate the differences across groups." (Greenland et al. 2016). This package, pTITAN2, enables comparing TITAN2 output between treatments by permuting the observed data between treatments and rerunning TITAN on the permuted data. There are some limitations on the permutations, including (1) a site cannot occur in a category more than once, the same limitation as in the original TITAN runs and (2) the original sample size distribution is maintained. This addresses potential sample size effects and enables comparisons between treatments with different sampling sizes.