R: Calculate and plot maps

connectivity {geohabnet}

R Documentation

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, 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