biodecrypt.optimise: Comparing the values obtained by biodecrypt.wrap, it...

In leondap/recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Comparing the values obtained by biodecrypt.wrap, it optimises the combination of alpha, buffer and ratio values to be used with biodecrypt function.

Description

The function biodecrypt.optimise analyses the output of biodecrypt.wrap. By default, a combination of MIR^2+NIR+NUR is used as a penalty value for the different combinations of the parameters (providing a higher importance to MIR). The exponents can be changed by the user. Since the method showing the lowest penalty in cross-validation might not necessarily be the optimal value for the final analysis, all the combinations showing a penalty value not higher than a certain threshold compared with the analysis showing the lowest penalty should be considered as similarly good. We provided a value of 10 as a default, representing a variation of about 3 for each addendum of the penalty. The optimal parameters can then be calculated as mean values of distance ratio, alpha and buffer among those used in these cross-validation analyses, weighted by 1/penalty in order to provide an increasing contribution to the solutions showing the lowest penalty values.

Usage

biodecrypt.optimise(tab,coef=c(2,1,1), penalty=10)

Arguments

tab	A matrix obtained with biodecrypt.wrap.
coef	The three exponents to be applied to MIR, NIR and NUR, respectively, to calculate the penalties.
penalty	The penalty threshold for inclusion in the calculation.

Value

ratio	The optimized ratio value.
buffer	The optimized buffer value.
alpha	The optimized alpha value.
MIR	The weighted average MIR among selected combinations.
NIR	The weighted average MIR among selected combinations.
NUR	The weighted average MIR among selected combinations.

Author(s)

Leonardo Dapporto

References

Platania L. et al. Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies. Glocal Ecology and Biogeography (2020).

Examples

#See the example provided in biodecrypt.wrap

leondap/recluster documentation built on Nov. 11, 2024, 7:11 a.m.