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Jackknifing is a technique for estimating the standard error associated with an estimate such as a diversity or evenness index.
When any of the appropriate alpha diversity or evenness measures is selected within Species Diversity and Richness jackknife estimate of the standard error for the combined (all sample) index will be given at the bottom of the output (see below).
For this Jackknife estimate to have meaning all of the samples included in the calculation must be replicates all from the same habitat. To select the samples for inclusion in the jackknifing procedure see Selecting Samples to Analyse.
See How jackknifing works for details of the computation method.
Strictly speaking jackknifing cannot be used to calculate confidence intervals, just standard errors and bias. A boot strap must be used for confidence intervals.