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

Internal Name

BioDinamica