Calculates the standardized effect size for
functional and phylogenetic alpha diversity.
See bootspat_str and
bootspat_naive
Usage
spat.rand(
x,
tree,
aleats,
random = c("site", "species", "both", "spat"),
cores = 1,
filename = "",
...
)Arguments
- x
SpatRaster. A SpatRaster containing presence-absence data (0 or 1) for a set of species.
- tree
It can be a 'data.frame' with species traits or a 'phylo' with a rooted phylogenetic tree. Species names in 'tree' and 'x' must match!
- aleats
positive integer. A positive integer indicating how many times the calculation should be repeated.
- random
character. A character indicating the type of randomization. The currently available randomization methods are "spat", "site", "species" or "both" (site and species).
- cores
positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used.
- filename
character. Output filename.
- ...
additional arguments to be passed passed down from a calling function.
Examples
# \donttest{
x <- terra::rast(system.file("extdata", "ref.tif",
package = "divraster"))
traits <- read.csv(system.file("extdata", "traits.csv",
package = "divraster"), row.names = 1)
tree <- ape::read.tree(system.file("extdata", "tree.tre",
package = "divraster"))
spat.rand(x, tree, 3, "site")
#> class : SpatRaster
#> dimensions : 8, 8, 4 (nrow, ncol, nlyr)
#> resolution : 0.125, 0.125 (x, y)
#> extent : 0, 1, 0, 1 (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 : 4.217869, 0.05263325, 3.359948, -9.313514
#> max values : 9.524013, 1.26248756, 10.571964, 10.454383
spat.rand(x, traits, 3, "site")
#> class : SpatRaster
#> dimensions : 8, 8, 4 (nrow, ncol, nlyr)
#> resolution : 0.125, 0.125 (x, y)
#> extent : 0, 1, 0, 1 (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 : 0.3846142, 0.02100142, 0.3492543, -3.832472
#> max values : 1.2542336, 0.25886931, 1.2493508, 8.094669
# }