connectivity: Calculate and plot maps

In geohabnet: Geographical Risk Analysis Based on Habitat Connectivity

Calculate and plot maps

Description

Calculate mean, variance and difference. The result is produced in form of maps plotted with predefined settings. Currently, the settings for plot cannot be customized. Default value is TRUE for all logical arguments

Usage

connectivity(
  host,
  indices,
  global = FALSE,
  east = NULL,
  west = NULL,
  geoscale = NULL,
  res = reso(),
  pmean = TRUE,
  pvar = TRUE,
  pdiff = TRUE,
  outdir = tempdir()
)

Arguments

host	SpatRaster. Host density map aka SpatRaster object
indices	SpatRaster. Collection of risk indices.
global	Logical. TRUE if global analysis is desired, FALSE otherwise. east and west are required when TRUE.
east	SpatRaster. Collection of risk indices on eastern extent.
west	SpatRaster. Collection of risk indices on western extent. When TRUE, geoscale is ignored. Default is TRUE.
geoscale	Vector. geographical scale. Default is NULL.
res	Numeric. Map resolution. This value is used in aggregation and dis-aggregation operation. Default is reso().
pmean	Logical. TRUE if map of mean should be plotted, FALSE otherwise.
pvar	Logical. TRUE if variance map should be plotted, FALSE otherwise.
pdiff	Logical. TRUE if difference map should be plotted, FALSE otherwise.
outdir	Character. Output directory for saving raster in TIFF format. Default is tempdir().

Details

indexes are actually risk indices i.e. lis of spatRaster objects resulting from operations on crop's raster and parameters provided in either parameters.yaml or sean().

It will save all the opted plots using - pmean, pvar and pdiff. File will be saved in provided value of outdir or tempdir().If interactive() is TRUE, then plots can be seen in active plot window. E.g. Rstudio. The maps are plotted using SpatRaster object. These objects are available as a return value of this function.

Value

Gmap. See details.

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

hci_mean(), hci_variance(), hci_diff()

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