coherence: Coherence metrics

In prior3D: 3D Prioritization Algorithm

Coherence metrics

Description

Coherence metrics

Usage

coherence(x, w, metric = "sa", normalize = TRUE, plot = TRUE, addlines = TRUE, ...)

Arguments

x	Output of Compare_2D_3D function.
w	Integer indicating square window dimensions.
metric	Cohension metric to use. It must be one of "sa", "sku" and "rao"
normalize	If TRUE, then sum of solutions is normalized at a [0,1] scale.
plot	If TRUE, then coherence maps are ploted.
addlines	If TRUE, then border lines from maps::map are ploted.
...	Further arguments passed in function, based on metric choice. See more in Details.

Details

"sa" and "sku" are derived from geodiv::focal_metrics and in ellipsis (...) further arguments of geodiv::focal_metrics are passed.

metric = "rao" is derived from rasterdiv::paRao and in ellipsis (...) further arguments of rasterdiv::paRao are passed.

Value

numeric vector with 2D and 3D metrics. The result maps are optionally ploted.

References

Rocchini, Duccio, Matteo Marcantonio, Daniele Da Re, Giovanni Bacaro, Enrico Feoli, Giles Foody, Reinhard Furrer, et al. 2021. "From zero to infinity: Minimum to maximum diversity of the planet by spatio-parametric Rao’s quadratic entropy." Global Ecology and Biogeography 30 (5): 2315. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/geb.13270")}.

Rocchini, Duccio, Elisa Thouverai, Matteo Marcantonio, Martina Iannacito, Daniele Da Re, Michele Torresani, Giovanni Bacaro, et al. 2021. "rasterdiv - An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back." Methods in Ecology and Evolution 12 (6): 2195. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/2041-210X.13583")}.

Smith, Annie C., Phoebe Zarnetske, Kyla Dahlin, Adam Wilson, and Andrew Latimer. 2023. Geodiv: Methods for Calculating Gradient Surface Metrics. https://CRAN.R-project.org/package=geodiv.

Becker OScbRA, Minka ARWRvbRBEbTP, Deckmyn. A (2023). maps: Draw Geographical Maps. R package version 3.4.2, https://CRAN.R-project.org/package=maps

See Also

Compare_2D_3D

Examples

## Not run: 
## This example requires commercial solver from 'gurobi' package for
## portfolio = "gap". Else replace it with e.g. portfolio = "shuffle" for using
## a free solver like the one from 'highs' package.

biodiv_raster <- get_biodiv_raster()
depth_raster <- get_depth_raster()
data(biodiv_df)

out_2D_3D <- Compare_2D_3D(biodiv_raster = biodiv_raster,
                           depth_raster = depth_raster,
                           breaks = c(0, -40, -200, -2000, -Inf),
                           biodiv_df = biodiv_df,
                           budget_percents = seq(0, 1, 0.1),
                           budget_weights = "richness",
                           threads = parallel::detectCores(),
                           portfolio = "gap",
                           portfolio_opts = list(number_solutions = 10))

coherence(out_2D_3D, w = 3, metric = "sa")
coherence(out_2D_3D, w = 3, metric = "sku")
coherence(out_2D_3D, w = 3, metric = "rao")

## End(Not run)

prior3D documentation built on April 11, 2025, 5:39 p.m.