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

===== Group =====

[[BioDinamica | BioDinamica]]


===== Internal Name =====

BioDinamica