sa_onrasters: Run sensitivity analysis

In geohabnet: Geographical Risk Analysis Based on Habitat Connectivity

Run sensitivity analysis

Description

Same as sensitivity_analysis() but it takes raster object and other parameters as an input.

• sa_onrasters() is a wrapper around sean() function. Takes raster object and other parameters as an input.

• msean_onrast() same as sa_onrasters(). Use this for side effects + results. Produces and plots the maps for the outcomes and results are returned as an object. It produces and plots the maps for the outcomes and results are returned as an object.

Usage

sa_onrasters(rast, link_thresholds = c(0), hd_thresholds = c(0), ...)

msean_onrast(
  global = TRUE,
  geoscale = NULL,
  res = reso(),
  outdir = tempdir(),
  ...
)

Arguments

rast	Raster object which will be used in analysis.
link_thresholds	Numeric vector. link threshold values
hd_thresholds	Numeric vector. host density threshold values
...	Additional parameters to be passed to sean().
global	Logical. TRUE if global analysis, FALSE otherwise. Default is TRUE
geoscale	Numeric vector. Geographical coordinates in the form of c(Xmin, Xmax, Ymin, Ymax) which EPSG:4326 in coordinate reference system. If geoscale is NuLL, the extent is extracted from rast(SpatRaster) using terra::ext().
res	Numeric. Resolution of the raster. Default is reso().
outdir	Character. Output directory for saving raster in TIFF format. Default is tempdir().

Details

Error not handled for non-overlapping extents.

Value

A list of calculated CCRI indices after operations. An index is generated for each combination of paramters. One combination is equivalent to sean() function.

References

Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory A Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen A Garrett, Global Cropland connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/biosci/biaa067")}

Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra

See Also

Use get_rasters() to obtain raster object.

msean_onrast() supported_sources()

Examples

rr <- get_rasters(list(monfreda = c("avocado")))
res1 <- sa_onrasters(rr[[1]],
            global = FALSE,
            geoscale = c(-115, -75, 5, 32),
            c(0.0001, 0.00004),
            c(0.0001, 0.00005),
            c("sum", "mean"),
            res = 12)
res2 <- sa_onrasters(rr[[1]],
            global = TRUE,
            link_thresholds = c(0.000001),
            hd_thresholds = c(0.00015),
            agg_methods = c("sum"),
            res = 12)
res3 <- msean_onrast(rast = rr[[1]],
          link_thresholds = c(0.000001),
          hd_thresholds = c(0.00015))

geohabnet documentation built on June 27, 2024, 5:11 p.m.