Introduction

Macroecological studies have been increasingly utilized in the context of climate change, necessitating the use of tools to analyze large datasets. To examine and comprehend the intricate mechanisms that underlie species distributions and the structure of biological communities, a diverse array of metrics has been developed. These metrics encompass alpha and beta diversity patterns across taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions. The package divraster addresses a current gap in this field by offering functions to calculate diversity metrics directly from rasters, eliminating the need for matrix transformations. This capability is especially valuable when dealing with extensive datasets, as matrices often impose memory constraints.

Installation

If you find any bug, let us know through divraster Issues. The development version of divraster can be installed from the divraster repository in Github:

require(devtools)
devtools::install_github("flaviomoc/divraster", build_vignettes = TRUE)

Analysis

The divraster package can directly calculate temporal beta diversity from multilayer rasters for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions using the temp.beta() function. To our knowledge this method has not been previously implemented in R. Furthermore, divraster can compute spatial alpha and beta diversity for TD, FD, and PD by using the spat.alpha() and spat.beta() functions. All beta diversity calculations are partitioned into replacement and richness differences components. Additionally, the spat.trait() function calculates individual average traits of continuous variables, while the spat.rand() calculates standardized effect size for FD and PD alpha diversity.

Let’s see some examples.

Loading data

# Presence-absence SpatRaster
bin1 <- terra::rast(system.file("extdata", 
                                "ref_frugivor.tif", 
                                package = "divraster"))
bin2 <- terra::rast(system.file("extdata", 
                                "fut_frugivor.tif", 
                                package = "divraster"))

# Change extension to process faster
terra::ext(bin1)
#> SpatExtent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax)
e <- c(-41, -39, -15, -13)
bin1 <- terra::crop(bin1, e)
bin2 <- terra::crop(bin2, e)

# Species traits
traits <- read.csv(system.file("extdata", 
                               "traits_frugivor.csv", 
                               package = "divraster"), 
                   sep = ";", 
                   row.names = 1)

# Phylogenetic tree
tree <- ape::read.tree(system.file("extdata", 
                                   "tree_frugivor.tre", 
                                   package = "divraster"))

Alpha diversity

# Taxonomic
alpha.td <- divraster::spat.alpha(bin1)
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#>      (status 2 uses the sf package in place of rgdal)
alpha.td
#> class       : SpatRaster 
#> dimensions  : 16, 16, 1  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> name        : Alpha_TD 
#> min value   :        0 
#> max value   :       67
terra::plot(alpha.td, main = names(alpha.td))


# Functional
alpha.fd <- divraster::spat.alpha(bin1, traits)
alpha.fd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 1  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> name        : Alpha_FD 
#> min value   : 3.723151 
#> max value   : 4.378846
terra::plot(alpha.fd, main = names(alpha.fd))


# Phylogenetic
alpha.pd <- divraster::spat.alpha(bin1, tree)
alpha.pd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 1  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> name        : Alpha_PD 
#> min value   : 1523.921 
#> max value   : 1859.668
terra::plot(alpha.pd, main = names(alpha.pd))

Average traits

avg.traits1 <- divraster::spat.trait(bin1, traits)
avg.traits1
#> class       : SpatRaster 
#> dimensions  : 16, 16, 12  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       : Beak.~ulmen, Beak.~Nares, Beak.Width, Beak.Depth, Tarsu~ength, Wing.Length, ... 
#> min values  :    22.12692,    14.00385,   7.046154,   8.526923,    25.15000,    117.0016, ... 
#> max values  :    24.52903,    16.41452,   7.804545,   9.601515,    26.29828,    122.0379, ...
terra::plot(avg.traits1, main = names(avg.traits1))

Standardize Effect Size

# Functional
ses.fd <- divraster::spat.rand(bin1, traits, 3, "site")
ses.fd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 4  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :  Mean_FD,       SD_FD, Observed_FD,     SES_FD 
#> min values  : 3.804965, 0.004442342,    3.723151, -11.491807 
#> max values  : 4.429896, 0.218169533,    4.378846,   2.366919
terra::plot(ses.fd, main = names(ses.fd))


# Phylogenetic
ses.pd <- divraster::spat.rand(bin1, tree, 3, "site")
ses.pd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 4  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :  Mean_PD,     SD_PD, Observed_PD,     SES_PD 
#> min values  : 1571.430,  1.016952,    1623.451, -24.449621 
#> max values  : 1873.683, 67.345810,    1880.676,   9.213572
terra::plot(ses.pd, main = names(ses.pd))

Spatial beta diversity

# Taxonomic
beta.td <- divraster::spat.beta(bin1)
beta.td
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :   Btotal_TD,   Brepl_TD,    Brich_TD 
#> min values  : 0.006060606, 0.00000000, 0.004264392 
#> max values  : 0.109409606, 0.03638009, 0.103181683
terra::plot(beta.td, main = names(beta.td))


# Functional
beta.fd <- divraster::spat.beta(bin1, traits)
beta.fd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :    Btotal_FD,   Brepl_FD,     Brich_FD 
#> min values  : 0.0004245858, 0.00000000, 0.0004245858 
#> max values  : 0.0793045655, 0.01846139, 0.0793045655
terra::plot(beta.fd, main = names(beta.fd))


# Phylogenetic
beta.pd <- divraster::spat.beta(bin1, tree)
beta.pd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :   Btotal_PD,    Brepl_PD,    Brich_PD 
#> min values  : 0.002851805, 0.000000000, 0.001618621 
#> max values  : 0.059656685, 0.008026876, 0.059656685
terra::plot(beta.pd, main = names(beta.pd))

Temporal beta diversity

# Taxonomic
betatemp.td <- divraster::temp.beta(bin1, bin2)
betatemp.td
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :  Btotal_TD,   Brepl_TD,   Brich_TD 
#> min values  : 0.02985075, 0.00000000, 0.02985075 
#> max values  : 0.31578947, 0.09836066, 0.31578947
terra::plot(betatemp.td, main = names(betatemp.td))


# Functional
betatemp.fd <- divraster::temp.beta(bin1, bin2, traits)
betatemp.fd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       :  Btotal_FD,   Brepl_FD,   Brich_FD 
#> min values  : 0.01733908, 0.00000000, 0.01012696 
#> max values  : 0.17031569, 0.03741327, 0.17031569
terra::plot(betatemp.fd, main = names(betatemp.fd))


# Phylogenetic
betatemp.pd <- divraster::temp.beta(bin1, bin2, tree)
betatemp.pd
#> class       : SpatRaster 
#> dimensions  : 16, 16, 3  (nrow, ncol, nlyr)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -41, -39, -15, -13  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       : Btotal_PD,  Brepl_PD,    Brich_PD 
#> min values  : 0.0120217, 0.0000000, 0.009533166 
#> max values  : 0.1792291, 0.0394096, 0.179229119
terra::plot(betatemp.pd, main = names(betatemp.pd))

divraster Vignette

Flávio Mota