Phyogenetic Composition Interpolation

Description

This functor interpolates Phylogenetic beta-diversity index on the map.The method employed herein is analogous to that described by: Oliveira, U., Vasconcelos, M. F., & Santos, A. J. (2017). Biogeography of Amazon birds: rivers limit species composition, but not areas of endemism. Scientific Reports, 7(1), 2992. doi:10.1038/s41598-017-03098-w. However, here we apply the index of Phylogenetic Beta-Diversity. For more detaisl about index, see: Graham, C.H., Fine, P.V.A., 2008. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol. Lett. 11, 1265–1277. https://doi.org/10.1111/j.1461-0248.2008.01256.x

Inputs

Name	Type	Description
Input Occurences	csv file	Csv file with species occurences (colunms sp, x, y).
Input Phylogenetic Tree	tre file	Input filogenetic tree in format “.tre”
Input Mask	Map Filename Type	The filename of the shape of area of study.
Output folder	Folder	Folder to save outputs.
Beta Diversity Index	Real Value Type	Beta Diversity Index: 1-Bray-Curtis; 2-Jaccard
Save Hexagon Nmds	Boolean Value Type	The file of phylogenetic tree has branch lengths?
Spline Interpolation	Boolean Value Type	Save hexagon with raw values map?
Kriging Interpolation Lengths	Boolean Value Type	Interpolate by kriging?
The Tree Has Branch Lengths	Boolean Value Type	The file of phylogenetic tree has branch lengths?
The Tree Has Branch Lengths	Boolean Value Type	The file of phylogenetic tree has branch lengths?
The Tree Has Branch Lengths	Boolean Value Type	The file of phylogenetic tree has branch lengths?
Hexagon Size	Real Value Type	Value of Hexagon size
Beta Diversity Partition Analysis	Boolean Value Type	Beta diversity partition analysis (Turnover and Nestedness)
Cell Size	Real Value Type	Cell size of output raster
Number Of Axis	Real Value Type	Define number of axis in NMDS analysis
Rounds Of Nmds Search	Real Value Type	Maximum numbers of random starts in search
Minimum Number Of Sambles	Real Value Type	Minimum number of samples in hexagons
Smooth Factor Of Spline	Real Value Type	Number of neighboring pixels in smooth
Spline Lambda	Real Value Type	Smoothing parameter the ratio of error and process variance in spline interpolation
Model In Kriging Interpolation	Real Value Type	Specification of the variogram model: 1- spherical, 2- exponential, 3- gaussian
Lags In Kriging Interpolation	Real Value Type	Number of lags
Smooth Factor Of Kriging	Real Value Type	Number of neighboring pixels in smooth
Classify Spline	Boolean Value Type	Classify areas by unsupervised classification
Number Of Classes Of Spline	Real Value Type	Number of classes in classification
Classify Kriging	Real Value Type	Classify areas by unsupervised classification
Number Of Classes Of Kriging	Real Value Type	Number of classes in classification

Group

BioDinamica

Internal Name

BioDinamica