Package: phyloraster 2.1.0

phyloraster: Evolutionary Diversity Metrics for Raster Data

Phylogenetic Diversity (PD, Faith 1992), Evolutionary Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE, Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE, Laffan et al. 2016) for presence-absence raster. Faith, D. P. (1992) <doi:10.1016/0006-3207(92)91201-3> Isaac, N. J. et al. (2007) <doi:10.1371/journal.pone.0000296> Laffan, S. W. et al. (2016) <doi:10.1111/2041-210X.12513> Rosauer, D. et al. (2009) <doi:10.1111/j.1365-294X.2009.04311.x>.

Authors:Gabriela Alves-Ferreira [aut, cre, cph], Flávio M. M. Mota [aut], Neander Marcel Heming [aut]

# Install 'phyloraster' in R:

install.packages('phyloraster', repos = c('https://gabferreira.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On CRAN:

Last updated 1 months agofrom:928ab34d0c. Checks:OK: 7. Indexed: yes.

Gabriela Alves-Ferreira, Flávio Mota and Neander Heming

Last update: 2024-03-19
Started: 2023-06-14

Help page	Topics
Check for missing arguments in function call	arg.check
Presence-absence of 33 Australian tree frogs (Rosauer 2017)	dataR
Delta of Diversity Metrics	delta.grid
Transform a data.frame to raster	df2rast
Calculate phylogenetic community metrics for raster data	geo.phylo
Calculate phylogenetic community metrics and their standardized effect sizes for raster data	geo.phylo.ses
Calculate the inverse of range size	inv.range
Load an example dataset with presence-absence data of 33 tree frogs and a phylogenetic tree for this species	load.data.rosauer
Prepare rasters and phylogenetic tree to run community metrics	phylo.pres
Calculate range size for a set of species using a raster as input	range_size
Calculate Evolutionary distinctiveness for raster data	rast.ed
Evolutionary distinctiveness standardized for specie richness	rast.ed.ses
Calculate phylogenetic diversity for raster data	rast.pd
Phylogenetic diversity standardized for species richness	rast.pd.ses
Calculate phylogenetic endemism for raster data	rast.pe
Phylogenetic endemism standardized for specie richness	rast.pe.ses
Calculate species richness for raster data	rast.sr
Calculate weighted endemism for raster data	rast.we
Calculate weighted endemism standardized for species richness	rast.we.ses
Rasterize shapefile	shp2rast
Calculate Evolutionary distinctiveness for each species	species.ed
Compute species tip length	species.tip.length
Compute tree edge lengths and node paths from root to each tip	tip.root.path