Package 'geohabnet' reference manual

Title:	Geographical Risk Analysis Based on Habitat Connectivity
Description:	The geohabnet package is designed to perform a geographically or spatially explicit risk analysis of habitat connectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067> proposed the concept of cropland connectivity as a risk factor for plant pathogen or pest invasions. As the functions in geohabnet were initially developed thinking on cropland connectivity, users are recommended to first be familiar with the concept by looking at the Xing et al paper. In a nutshell, a habitat connectivity analysis combines information from maps of host density, estimates the relative likelihood of pathogen movement between habitat locations in the area of interest, and applies network analysis to calculate the connectivity of habitat locations. The functions of geohabnet are built to conduct a habitat connectivity analysis relying on geographic parameters (spatial resolution and spatial extent), dispersal parameters (in two commonly used dispersal kernels: inverse power law and negative exponential models), and network parameters (link weight thresholds and network metrics). The functionality and main extensions provided by the functions in geohabnet to habitat connectivity analysis are a) Capability to easily calculate the connectivity of locations in a landscape using a single function, such as sensitivity_analysis() or msean(). b) As backbone datasets, the geohabnet package supports the use of two publicly available global datasets to calculate cropland density. The backbone datasets in the geohabnet package include crop distribution maps from Monfreda, C., N. Ramankutty, and J. A. Foley (2008) <doi:10.1029/2007gb002947> "Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000, Global Biogeochem. Cycles, 22, GB1022" and International Food Policy Research Institute (2019) <doi:10.7910/DVN/PRFF8V> "Global Spatially-Disaggregated Crop Production Statistics Data for 2010 Version 2.0, Harvard Dataverse, V4". Users can also provide any other geographic dataset that represents host density. c) Because the geohabnet package allows R users to provide maps of host density (as originally in Xing et al (2021)), host landscape density (representing the geographic distribution of either crops or wild species), or habitat distribution (such as host landscape density adjusted by climate suitability) as inputs, we propose the term habitat connectivity. d) The geohabnet package allows R users to customize parameter values in the habitat connectivity analysis, facilitating context-specific (pathogen- or pest-specific) analyses. e) The geohabnet package allows users to automatically visualize maps of the habitat connectivity of locations resulting from a sensitivity analysis across all customized parameter combinations. The primary function is sean() and sensitivity analysis(). Most functions in geohabnet provide as three main outcomes: i) A map of mean habitat connectivity across parameters selected by the user, ii) a map of variance of habitat connectivity across the selected parameters, and iii) a map of the difference between the ranks of habitat connectivity and habitat density. Each function can be used to generate these maps as 'final' outcomes. Each function can also provide intermediate outcomes, such as the adjacency matrices built to perform the analysis, which can be used in other network analysis. Refer to article at <https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html> to see examples of each function and how to access each of these outcome types. To change parameter values, the file called parameters.yaml stores the parameters and their values, can be accessed using get_parameters() and set new parameter values with set_parameters(). Users can modify up to ten parameters.
Authors:	Krishna Keshav [aut, cre], Aaron Plex [aut] , Garrett Lab [ctb] (https://garrettlab.com), Karen Garrett [aut] , University of Florida [cph, fnd] (https://www.ufl.edu)
Maintainer:	Krishna Keshav <[email protected]>
License:	GPL-3
Version:	2.1.3
Built:	2024-09-29 19:25:36 UTC
Source:	CRAN

Internal function to extract risk indices from a list of crop rasters.

Description

Internal function to extract risk indices from a list of crop rasters.

Usage

.indices(crop_rasters)
.indices(crop_rasters)

Arguments

crop_rasters

List of raster objects.

Value

A list of risk indices.

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()
)
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

Get raster object for crop

Description

Get cropland information in a form of raster object from data source for crop

Usage

cropharvest_rast(crop_name, data_source)
cropharvest_rast(crop_name, data_source)

Arguments

`crop_name`	Name of the crop
`data_source`	Data source for cropland information

Value

Raster.

Examples


cropharvest_rast("avocado", "monfreda")


cropharvest_rast("avocado", "monfreda")

Get sum of rasters for individual crops

Description

Takes crop names and returns raster object which is sum of raster of individual crops. Currently, only supports crops listed in geodata::monfredaCrops(), geodata::spamCrops() If crop is present in multiple sources, then their mean is calculated.

Usage

crops_rast(crop_names)
crops_rast(crop_names)

Arguments

crop_names

A named list of source along with crop names

Value

SpatRaster. Raster object which is sum of all the individual crop raster

Examples


crops_rast(list(monfreda = c("wheat", "barley"), mapspam2010 = c("wheat", "potato")))

crops_rast(list(monfreda = c("wheat", "barley"), mapspam2010 = c("wheat", "potato")))

Distance methods supported

Description

Contains supported strategies to calculate distance between two points. Use of one the methods in sean() or sensitivity_analysis().

Usage

dist_methods()
dist_methods()

Value

vector

Examples

dist_methods()

dist_methods()

GeoModel class

Description

A ref class to represent results of dispersal models.

Slots

amatrix: An adjacency matrix to represent network.
index: A raster object representing the index.
hdthreshold: A numeric value representing the threshold.
aggregation: A character value representing the aggregation method.
linkthreshold: A numeric value representing the link threshold.
beta: A numeric value representing the beta parameter.
gamma: A numeric value representing the gamma parameter.

GeoNetwork

Description

An S4 class representing a network of geographical data. This will wrap all the results from the risk analysis using sean() or sensitivity_analysis(). This class contains the field from Gmap class which has results in the form of SpatRaster and TIFF file.

Usage

## S4 replacement method for signature 'GeoNetwork'
host_density(x) <- value
## S4 replacement method for signature 'GeoNetwork'
host_density(x) <- value

Arguments

`x`	GeoNetwork.
`value`	SpatRaster.

Value

GeoNetwork.

Slots

rasters: A list of GeoRasters objects.
host_density: A SpatRaster representing the host density.
me_rast: A raster representing mean risk index.
me_out: Character. A file path to the mean risk index raster.
diff_rast: A raster representing difference.
diff_out: Character. A file path to the difference raster.
var_rast: A raster representing variance.
var_out: Character. A file path to the variance raster.

GeoRaster class

Description

A class to represent raster vis-a-vis risk indices. This class encapsulates the results of apply dispersal models and metrics.

Fields

host_density: SpatRaster. A spatial raster representing host density.
rasters: List. List of raster representing risk indices. These are of type GeoModels.
global: Boolean. True if contains GlobalRast object, False otherwise.

Get geographical scales from the parameters

Description

This function returns a list of geographical scales set in global and custom extent in parameters.yaml. If global is TRUE, the CustomExt is ignored.

Usage

geoscale_param(gparams = load_parameters())
geoscale_param(gparams = load_parameters())

Arguments

gparams

Optional. load_parameters() or null

Value

Vector. A set of geographical scales

Get Parameters

Description

This function retrieves the parameters and copies the parameter file to the specified output path.

Usage

get_parameters(out_path = tempdir(), iwindow = FALSE)
get_parameters(out_path = tempdir(), iwindow = FALSE)

Arguments

`out_path`	character. The output path where the parameter file will be copied. The default is a temporary directory `tempdir()`
`iwindow`	logical. If window = `TRUE`, this will prompt the user to select the output directory using a file chooser window. The default value is `FALSE`.

Details

Using configuration file is an alternative to sean()

Value

character. The path to the copied parameter file.

Examples

get_parameters()
get_parameters(out = tempdir())

get_parameters()
get_parameters(out = tempdir())

Get rasters object from parameters

Description

Takes named list of hosts as an input. See host object in get_parameters() or load_parameters(). This is also a wrapper of crops_rast(). Function creates 2 raster object - one is a sum of all the crops specified under sources and other using the provided raster file. See tiff_torast()

Usage

get_rasters(hosts)
get_rasters(hosts)

Arguments

hosts

List of hosts and values. It is synonym to Hosts object in parameters

Value

List of SpatRaster.

Examples

# Get default rasters
## Not run: 
get_rasters(list(mapspam2010 = c("wheat"), monfreda = c("avocado"), file = "some_raster.tif"))

## End(Not run)
# Get default rasters
## Not run: 
get_rasters(list(mapspam2010 = c("wheat"), monfreda = c("avocado"), file = "some_raster.tif"))

## End(Not run)

Global geographical extent

Description

This function provides the geographical extent used in a global analysis. This function returns the geographic extents of the eastern and western hemispheres used in the analysis. Each geographic extent is in the form of c(Xmin, Xmax, Ymin, Ymax). The geohabnet functions are designed to work with the coordinate reference system: lon/lat WGS 84 (EPSG:4326).

Usage

global_scales()
global_scales()

Details

When a habitat connectivity analysis is global, the functions in geohabnet will conduct two separate analyses, one on the geographical scale of the eastern hemisphere and another for the western hemisphere. The final outcomes (such as maps or adjacency matrices) are then combined for the global analysis.

Value

List. Named list with scales for eastern and western hemispheres

GlobalRast class

Description

A class to represent raster for global scales. Global scales are accessible using global_scales(). However, this class encapsulates the results of apply dispersal models and metrics.

Fields

east: A list of raster for eastern hemisphere.
west: A list of raster for western hemisphere.

Gmap class

Description

An S4 class to represent various maps in the form of SpatRaster.

Usage

setmaps(x, me, vari, dif)
setmaps(x, me, vari, dif)

Arguments

`x`	Gmap object.
`me`	SpatRaster. A raster representing mean risk index.
`vari`	SpatRaster. A raster representing variance.
`dif`	SpatRaster. A raster representing difference.

Value

Gmap object.

Slots

me_rast: A raster representing mean risk index.
me_out: Character. A file path to the mean risk index raster.
diff_rast: A raster representing difference.
diff_out: Character. A file path to the difference raster.
var_rast: A raster representing variance.
var_out: Character. A file path to the variance raster.

Plot a Raster* object

Description

This is a wrapper for terra::plot()

Usage

gplot(x, ...)
gplot(x, ...)

Arguments

`x`	a Raster* object
`...`	additional arguments passed to `terra::plot()`

Value

a plot

Examples

r <- terra::rast(nrows=108, ncols=21, xmin=0, xmax=10)
gplot(r)
gplot(r, col = "red")
gplot(r, col = "red", breaks = 10)
r <- terra::rast(nrows=108, ncols=21, xmin=0, xmax=10)
gplot(r)
gplot(r, col = "red")
gplot(r, col = "red", breaks = 10)

Calculate difference map

Description

This function produces a map of difference b/w mean and sum indexes in rank of cropland harvested area fraction.

Usage

hci_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())
hci_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())

Arguments

`x`	SpatRaster.
`y`	SpatRaster.
`global`	Logical. `TRUE` if global analysis is desired, `FALSE` otherwise. `east` and `west` are required when `TRUE`.
`geoscale`	Numeric vector. `x` will be cropped to this extent.
`res`	Numeric. Map resolution. This value is used in aggregation and dis-aggregation operation. Default is `reso()`.
`outdir`	Character. Output directory for saving raster in TIFF format. Default is `tempdir()`.

Details

Ideally, the function is tested to yield desired results when length(which(y[] > 0)) > length(which(x[] > 0)).

Value

RiskMap. Contains result in the form of SpatRaster objects and file path of the saved maps.

Calculate mean of raster objects

Description

Wrapper for terra::mean(). Calculates mean of list of rasters.

Usage

hci_mean(
  indices,
  global = FALSE,
  east = NULL,
  west = NULL,
  geoscale = NULL,
  res = reso(),
  plt = TRUE,
  outdir = tempdir()
)
hci_mean(
  indices,
  global = FALSE,
  east = NULL,
  west = NULL,
  geoscale = NULL,
  res = reso(),
  plt = TRUE,
  outdir = tempdir()
)

Arguments

`indices`	List of SpatRasters. This input represents the spatial raster collection for which mean is to be calculated.
`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()`.
`plt`	`TRUE` if need to plot mean map, `FALSE` otherwise.
`outdir`	Character. Output directory for saving raster in TIFF format. Default is `tempdir()`.

Value

RiskMap. Contains result in the form of SpatRaster objects and file path of the saved maps.

Calculate variance of CCRI

Description

This function produces a map of variance of CCRI based on input parameters

Usage

hci_variance(
  indices,
  rast,
  global,
  east = NULL,
  west = NULL,
  geoscale,
  res = reso(),
  outdir = tempdir()
)
hci_variance(
  indices,
  rast,
  global,
  east = NULL,
  west = NULL,
  geoscale,
  res = reso(),
  outdir = tempdir()
)

Arguments

`indices`	SpatRaster. Collection of risk indices.
`rast`	SpatRaster. Template for variance output
`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()`.
`outdir`	Character. Output directory for saving raster in TIFF format. Default is `tempdir()`.

Value

RiskMap. Contains result in the form of SpatRaster objects and file path of the saved maps.

Set the host density.

Description

Sets the host density slot in the GeoNetwork object

Usage

host_density(x) <- value
host_density(x) <- value

Arguments

`x`	the GeoNetwork object.
`value`	SpatRaster.

Dispersal kernels

Description

-⁠[inv_powerlaw()]⁠ Get parameters and values pertaining to the inverse power law model. -⁠[neg_exp()]⁠ Get parameters and values pertaining to the negative exponential model.

Usage

inv_powerlaw(
  params = load_parameters(),
  betas = NULL,
  mets = NULL,
  we = NULL,
  linkcutoff = NULL
)

neg_expo(
  params = load_parameters(),
  gammas = NULL,
  mets = NULL,
  we = NULL,
  linkcutoff = NULL
)
inv_powerlaw(
  params = load_parameters(),
  betas = NULL,
  mets = NULL,
  we = NULL,
  linkcutoff = NULL
)

neg_expo(
  params = load_parameters(),
  gammas = NULL,
  mets = NULL,
  we = NULL,
  linkcutoff = NULL
)

Arguments

`params`	Object. This function uses the parameter values defined in `load_parameters()` by default. If `load_parameters()` is not provided, the function will require the user to specify all arguments as listed below. If both `load_parameters()` and values for the arguments listed below are provided, `load_parameters()` takes precedence over the specified arguments.
`betas`	Numeric. Beta is the dispersal parameter used in the inverse power law to estimate a species' dispersal gradient. Please refer to Mundt et al (2009) for details on how to calculate this parameter. Any beta values should be positive. Smaller beta values indicate a higher likelihood of dispersal between nodes.
`mets`	Character. There are seven network metrics supported by `geohabnet`: "node_strength", "sum_of_nearest_neighbors", "eigenvector_centrality", "closeness", "betweeness", "degree", and "page_rank". Each specified network metric is calculated for each location in the target region, based on the link weights between each pair of locations. Run, for example, `pagerank()` for details of each network metric.
`we`	Numeric. This parameter indicates the weight(s) of each specified network metric, representing the importance of the network metric in the analysis. Since these weights represent percentages, any weight(s) should be between 0 and 100, and the sum of all specified weights should be 100.
`linkcutoff`	Numeric. This parameter is only used to calculate `betweeness()` and `closeness()`, and is equivalent to `cutoff` in these functions in the `igraph` package.
`gammas`	Numeric. Gamma is the dispersal parameter used in the negative exponential to estimate a species' dispersal gradient. Any gamma values should be positive. Smaller gamma values indicate a higher likelihood of dispersal between nodes.

Details

Refer to Esker et al (2007) for a discussion on the characteristics of each dispersal gradient or kernel model (i.e., inverse power law and negative exponential). The resulting object produced by load_parameters() provides the following values used when running the analysis -beta is a dispersal parameter for calculating the inverse power law model. -gamma is a dispersal parameter for calculating the negative exponential model. -metrics Each network metric is applied to the adjacency matrix produced in the intermediate step. -weights The link weights that is used in the network analysis. -cutoff Currently used as a parameter to calculate centrality in the network - betweeness() and closeness(). As defined in igraph::betweenness(), it's the maximum length to consider when calculating centrality. If zero or negative, then there is no such limit.

Value

List with parameters and values. See details.

References

Esker PD, Sparks AH, Antony G, Bates M, Dall' Acqua W, Frank EE, Huebel L, Segovia V, Garrett KA (2007). “Ecology and Epidemiology in R: Modeling dispersal gradients.” The Plant Health Instructor. doi:10.1094/PHI-A-2008-0129-03

Mundt CC, Sackett KE, Wallace LD, Cowger C, Dudley JP (2009). “Aerial Dispersal and Multiple-Scale Spread of Epidemic Disease.” Ecohealth. doi:10.1007/s10393-009-0251-z

Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.

Csárdi G, Nepusz T, Traag V, Horvát Sz, Zanini F, Noom D, Müller K (2024). igraph: Network Analysis and Visualization in R. doi:10.5281/zenodo.7682609, R package version 1.5.1, https://CRAN.R-project.org/package=igraph.

Load Parameters from YAML File

Description

This function loads parameters from a YAML file and stores them in an object.

Usage

load_parameters(filepath = .param_fp())
load_parameters(filepath = .param_fp())

Arguments

filepath

Path to the YAML file containing the parameters. By default, it takes the value of parameters.yaml in R user's directory.

Value

object with parameters and values

Examples

# Load parameters from default file
load_parameters()

# Load parameters from default file
load_parameters()

Supported sources for Mapspam

Description

Supported sources for Mapspam

Usage

mapspam()
mapspam()

Supported sources for monfreda

Description

Supported sources for monfreda

Usage

monfreda()
monfreda()

Network density

Description

Calculates and plots the network density of a GeoNetwork object.

Usage

ndplot(x)
ndplot(x)

Arguments

`x`	A GeoNetwork object

Value

Vector. Up to two ggplot2 objects

Network density

Description

Calculates and plots the network density of a GeoNetwork object. The plot is produced as dispersal parameter vs edge density.

Usage

## S4 method for signature 'GeoNetwork'
ndplot(x)
## S4 method for signature 'GeoNetwork'
ndplot(x)

Arguments

`x`	A GeoNetwork object

Value

Vector. Up to two ggplot2 objects

Calculation on network metrics a.k.a centralities.

Description

These are functions under the igraph package adapted to calculate habitat connectivity. In the context of habitat connectivity, the functions can be interpreted as follows:

nn_sum(): Calculates the sum of nearest neighbors igraph::knn().
node_strength(): Calculates the sum of edge weights of adjacent nodes igraph::strength().
betweenness(): Calculates the node betweenness based on the number of shortest paths. Because the igraph::betweenness() function in interprets link weights as distances to calculate the shortest paths, the betweeness() function in geohabnet transforms the link weights (or the relative likelihood of pathogen or pest movement) in the adjacency matrix so that higher link weight values will be the shortest (or more likely) paths for pathogen or pest movement.
ev(): Calculates the eigenvector centrality of positions within the network igraph::eigen_centrality().
closeness(): measures how many steps is required to access every other vertex from a given vertex igraph::closeness(). Because the igraph::closeness() function interprets link weights as distances to calculate the shortest paths, this transforms the link weights (or the relative likelihood of pathogen or pest movement) in the adjacency matrix so that higher link weight values will be the shortest (or more likely) paths for pathogen or pest movement.
degree(): number of adjacent edges igraph::degree().
pagerank(): page rank score for vertices igraph::page_rank().

Usage

nn_sum(crop_dm, ...)

node_strength(crop_dm, ...)

betweeness(crop_dm, ...)

ev(crop_dm, ...)

degree(crop_dm, ...)

closeness(crop_dm, ...)

pagerank(crop_dm, ...)
nn_sum(crop_dm, ...)

node_strength(crop_dm, ...)

betweeness(crop_dm, ...)

ev(crop_dm, ...)

degree(crop_dm, ...)

closeness(crop_dm, ...)

pagerank(crop_dm, ...)

Arguments

`crop_dm`	A square adjacency matrix, in which rows and columns names represent nodes (or locations) and each entry indicate the relative likelihood of pathogen or pest movement between a pair of nodes. In the internal workflow, the adjacency matrix comes as a result of operations within `sean()` function. This weight represents the importance of the network metric in the habitat connectivity analysis.
`...`	arguments to corresponding funtions in `igraph`

Value

SpatRaster. Representing connectivity of each node or location.

References

Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.

Reset parameters.yaml

Description

Resets the values in the parameters.yaml file to the default initial values.

Usage

reset_params()
reset_params()

Value

Logical. TRUE if function was successfully executed

Examples

reset_params()

reset_params()

Get resolution value

Description

Resolution stored in parameter.yaml. Here, resolution values refer to the aggregation factor or granularity. Granularity is the number of small grid cells that are aggregated into larger grid cells in each direction (horizontally and vertically). For example, the finest spatial resolution of the Monfreda and MAPSPAM datasets in geohabnet is 5 minutes, a granularity value of 6 will result in maps with a spatial resolution of 0.5 degrees. If not provided, the resolution value used for the analysis is by default 24 (or two degrees when using the Monfreda and MAPSPAM datasets). Otherwise, a single integer value for granularity equal to or greater than one should be specified.

Usage

reso()
reso()

Value

Numeric. Resolution from parameters.yaml. The default is 12.

Get risk indices

Description

Get risk indices from GeoRasters object.

Usage

risk_indices(ri)
risk_indices(ri)

Arguments

`ri`	GeoRasters object

Details

This function will unpack SpatRasters from GeoModel and thus is future::future() safe.

Value

List of risk indices. If the ri is global, the list will contain two elements, one for each hemisphere. e.g. list(east = list(), west = list()). If the ri is not global, the list will contain a single element, e.g. list().

RiskMap class

Description

An S4 class representing resulting maps from the specific operation type.

Fields

map: Character. A file path to the map.
riid: SpatRaster. This is one of the risk maps.
spr: SpatRaster. A spatial raster representing the risk index.
fp: Character. A file path to the risk index raster.

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(),
  ...
)
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

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

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))

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))

Sensitivity analysis across maps of habitat connectivity

Description

This function performs a sensitivity analysis across different values of habitat connectivity for each location in a map. For each combination of selected parameters, an index of habitat connectivity is calculated. sensitivity_analysis() is a wrapper around sean() function.

msean() is a wrapper around sean() function. It has additional argument to specify maps which are calculated using connectivity() function. The maps are essentially the risk network.

Usage

sean(
  rast,
  global = TRUE,
  geoscale = NULL,
  agg_methods = c("sum", "mean"),
  dist_method = "geodesic",
  link_threshold = 0,
  hd_threshold = 0,
  res = reso(),
  inv_pl = inv_powerlaw(NULL, betas = c(0.5, 1, 1.5), mets = c("betweeness",
    "NODE_STRENGTH", "Sum_of_nearest_neighbors", "eigenVector_centrAlitY"), we = c(50,
    15, 15, 20), linkcutoff = -1),
  neg_exp = neg_expo(NULL, gammas = c(0.05, 1, 0.2, 0.3), mets = c("betweeness",
    "NODE_STRENGTH", "Sum_of_nearest_neighbors", "eigenVector_centrAlitY"), we = c(50,
    15, 15, 20), linkcutoff = -1)
)

msean(
  rast,
  global = TRUE,
  geoscale = NULL,
  res = reso(),
  ...,
  outdir = tempdir()
)
sean(
  rast,
  global = TRUE,
  geoscale = NULL,
  agg_methods = c("sum", "mean"),
  dist_method = "geodesic",
  link_threshold = 0,
  hd_threshold = 0,
  res = reso(),
  inv_pl = inv_powerlaw(NULL, betas = c(0.5, 1, 1.5), mets = c("betweeness",
    "NODE_STRENGTH", "Sum_of_nearest_neighbors", "eigenVector_centrAlitY"), we = c(50,
    15, 15, 20), linkcutoff = -1),
  neg_exp = neg_expo(NULL, gammas = c(0.05, 1, 0.2, 0.3), mets = c("betweeness",
    "NODE_STRENGTH", "Sum_of_nearest_neighbors", "eigenVector_centrAlitY"), we = c(50,
    15, 15, 20), linkcutoff = -1)
)

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

Arguments

`rast`	Raster object which will be used in analysis.
`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()`.
`agg_methods`	Character. One or both the values - SUM, MEAN. Aggregation strategy for scaling the input raster to the desired resolution.
`dist_method`	Character. The method to calculate the distance matrix.
`link_threshold`	Numeric. A threshold value for link weight. All link weights that are below this threshold will be replaced with zero for the connectivity analysis. Link weights represent the relative likelihood of pathogen, pest, or invasive species movement between a pair of host locations, which is calculated using gravity models based on host density (or availability) and dispersal kernels.
`hd_threshold`	Numeric. A threshold value for host density. All locations with a host density below the selected threshold will be excluded from the connectivity analysis, which focuses the analysis on the most important locations. The values for the host density threshold can range between 0 and 1; if value is 1, all locations will be excluded from the analysis and 0 will include all locations in the analysis. Selecting a threshold for host density requires at least knowing what is the maximum value in the host density map to avoid excluding all locations in the analysis. if value is 1, all locations will be excluded from the analysis and 0 will include all locations in the analysis. Selecting a threshold for host density requires at least knowing what is the maximum value in the host density map to avoid excluding all locations in the analysis.
`res`	Numeric. Resolution of the raster. Default is `reso()`.
`inv_pl`	List. A named list of parameters for inverse power law. See details.
`neg_exp`	List. A named list of parameters for inverse negative exponential. See details. All locations with a host density below the selected threshold will be excluded from the connectivity analysis, which focuses the analysis on the most important locations. The values for the host density threshold can range between 0 and 1;
`...`	arguments passed to `sean()`
`outdir`	Character. Output directory for saving raster in TIFF format. Default is `tempdir()`.

Details

When global = TRUE, geoscale is ignored and global_scales() is used by default.

The functions sean() and msean() perform the same sensitivity analysis, but they differ in their return value. The return value of msean() is GeoNetwork, which contains the result from applying the connectivity() function on the habitat connectivity indexes. Essentially, the risk maps.

If neither the inverse power law nor the negative exponential dispersal kernel is specified, the function will return an error.

In msean(), three spatRasters are produced with the following values. For each location in the area of interest, the mean in habitat connectivity across selected parameters is calculated. For each location in the area of interest, the variance in habitat connectivity across selected parameters is calculated. For each location in the area of interest, the difference between the rank of habitat connectivity and the rank of host density is calculated. By default, each of these spatRasters is plotted for visualization.

Value

GeoRasters.

GeoNetwork.

References

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

Examples


avocado <- cropharvest_rast("avocado", "monfreda")

# global
ri <- sean(avocado) # returns a list of GeoRasters
mri <- msean(rast = avocado) # returns GeoNetwork object

# non-global
# geoscale is a vector of xmin, xmax, ymin, ymax

# returns GeoRasters object
ri <- sean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))
ri

# returns GeoNetwork object
mri <- msean(rast = avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))
mri

avocado <- cropharvest_rast("avocado", "monfreda")

# global
ri <- sean(avocado) # returns a list of GeoRasters
mri <- msean(rast = avocado) # returns GeoNetwork object

# non-global
# geoscale is a vector of xmin, xmax, ymin, ymax

# returns GeoRasters object
ri <- sean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))
ri

# returns GeoNetwork object
mri <- msean(rast = avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))
mri

Search for crop

Description

It returns the dataset sources in which crop data is available. Essentially, a wrapper around geodata::spamCrops() and geodata::monfredaCrops()

Usage

search_crop(name)
search_crop(name)

Arguments

name

name of crop

Value

Logical. Sources iin crop data is available.

Examples

search_crop("coffee")
search_crop("wheat")

search_crop("jackfruit")


search_crop("coffee")
search_crop("wheat")

search_crop("jackfruit")

Sensitivity analysis for habitat connectivity

Description

This function runs a sensitivity analysis on habitat connectivity calculated based on every combination of selected parameters. Parameter values in sensitivity_analysis() should be provided using the function set_parameters(). If no parameters are provided, then the sensitivity_analysis() function will run the sensitivity analysis using a default set of parameter values, which is accessible through the function get_parameters(). To customize parameter values, open the parameters.yaml that was automatically downloaded when geohabnet was installed, change, remove, or add parameter values directly in the parameters.yaml and save it. Once the values have been changed manually, run set_parameters() to set the new parameter values, which will return TRUE if the parameters were set successfully.

Usage

sensitivity_analysis(maps = TRUE, alert = TRUE)
sensitivity_analysis(maps = TRUE, alert = TRUE)

Arguments

`maps`	logical. `TRUE` if maps of outcomes are to be plotted, `FALSE` otherwise. If `TRUE`, three maps are possible: a map of mean habitat connectivity, a map of variance of habitat connectivity, and a map of the difference between the ranks in habitat connectivity and habitat density.
`alert`	logical. `TRUE` if a beep sound is to be played once the analysis is completed, `FALSE` otherwise

Details

For each location in a region, sensitivity_analysis() calculates the habitat connectivity risk index (CCRI) proposed by Xing et al. (2021). By default, sensitivity_analysis() runs a sensitivity analysis on a global extent, see global_scales() for details. This function also plots maps of the outcomes automatically, but it will suppress maps for outcomes if maps = FALSE or interactive() is FALSE. The returned object is of class GeoNetwork, which contains two types of outcomes. One outcome type corresponds to spatRasters representing the maps of habitat connectivity. The second type corresponds to adjacency matrices used to calculate the habitat connectivity, where columns and rows represent locations in the maps and entries are the relative likelihood of pathogen or pest movement between each pair of nodes.

Value

GeoNetwork. Errors are not handled.

References

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

Examples


# Run analysis on specified parameters.yaml
ss1 <- sensitivity_analysis()
ss2 <- sensitivity_analysis(FALSE, FALSE)
ss3 <- sensitivity_analysis(TRUE, FALSE)

# Run analysis on specified parameters.yaml
ss1 <- sensitivity_analysis()
ss2 <- sensitivity_analysis(FALSE, FALSE)
ss3 <- sensitivity_analysis(TRUE, FALSE)

Set global geographical extent

Description

This function sets the geographical extents used in global analysis. See also geoscale_param() to set the geographic extent of an analysis that is not global. Each geographic extent should be in the form of c(Xmin, Xmax, Ymin, Ymax). Geographic extent must be specified by four values in degrees that represent the geographic limits of the area for analysis, following the order: minimum longitude, maximum longitude, minimum latitude, and maximum latitude. Degrees are in decimal notation and have a negative sign for the southern and western hemispheres.

Usage

set_global_scales(value)
set_global_scales(value)

Arguments

value

list. Named list of eastern and western hemisphere extents. See usage.

Value

List. Named list with scales for eastern and western hemispheres

Examples

set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60)))
set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60)))

Set Parameters

Description

This function allows the user to set the parameters by replacing the existing parameters file with a new one. Use get_parameters() to modify the parameter values.

Usage

set_parameters(new_params, iwindow = FALSE)
set_parameters(new_params, iwindow = FALSE)

Arguments

`new_params`	The path to the new parameters file.
`iwindow`	Logical, indicating whether to prompt the user to select the new parameters file using a file selection window. The default value of this parameter is set to FALSE.

Value

None

Examples

param_fp <- get_parameters()
set_parameters(param_fp)

param_fp <- get_parameters()
set_parameters(param_fp)

Sets the map slots in the Gmap object.

Description

This wraps the results(SpatRasters) from the risk analysis.

Usage

## S4 method for signature 'Gmap'
setmaps(x, me, vari, dif)
## S4 method for signature 'Gmap'
setmaps(x, me, vari, dif)

Arguments

`x`	A Gmap object.
`me`	A GeoRaster object representing mean risk index.
`vari`	A GeoRaster object representing variance.
`dif`	A GeoRaster object representing difference.

Value

A Gmap object.

Set properties of the GeoModel object.

Description

Set properties of the GeoModel object.

Usage

setprops(x, aggregation, hdthreshold, linkthreshold)
setprops(x, aggregation, hdthreshold, linkthreshold)

Arguments

`x`	The GeoModel object.
`aggregation`	Character. A value representing the aggregation method.
`hdthreshold`	Numeric. A value representing the host density threshold.
`linkthreshold`	Numeric. A value representing the link threshold in a network.

Value

The GeoModel object with updated properties.

Set properties of the GeoModel object.

Description

Set properties of the GeoModel object.

Usage

## S4 method for signature 'GeoModel,character,numeric,numeric'
setprops(x, aggregation, hdthreshold, linkthreshold)
## S4 method for signature 'GeoModel,character,numeric,numeric'
setprops(x, aggregation, hdthreshold, linkthreshold)

Arguments

`x`	The GeoModel object.
`aggregation`	Character. A value representing the aggregation method.
`hdthreshold`	Numeric. A value representing the host density threshold.
`linkthreshold`	Numeric. A value representing the link threshold in a network.

Value

The GeoModel object with updated properties.

Raster for mapspam crop.

Description

get raster for crop in mapspam dataset

Usage

sp_rast(crp, africa = FALSE)
sp_rast(crp, africa = FALSE)

Arguments

`crp`	character. name of a crop. Case-insensitive.
`africa`	Fetch the 2017 Mpaspam crop data of Africa. Default is FALSE.

Details

See geodata::spamCrops() for supported crops.

Value

SpatRaster

References

International Food Policy Research Institute, 2020. Spatially-Disaggregated Crop Production Statistics Data in Africa South of the Sahara for 2017. <doi: 10.7910/DVN/FSSKBW>, Harvard Dataverse, V2

Examples


sp_rast("potato")
sp_rast("potato", TRUE)

sp_rast("potato")
sp_rast("potato", TRUE)

Returns metrics currently supported in the analysis.

Description

Returns metrics currently supported in the analysis.

Usage

supported_metrics()
supported_metrics()

Value

vector of supported metrics.

Examples

supported_metrics()

supported_metrics()

Get supported sources of crops

Description

When provided, cropharvest_rast() will look for cropland data in this specific source.

Usage

supported_sources()
supported_sources()

Value

Vector of supported sources. Also used as a lookup to find get raster object.

Examples

# Get currently supported sources
supported_sources()
# Get currently supported sources
supported_sources()

Get raster object from tif file

Description

This is a wrapper of terra::rast() and generates a raster object if provided with a TIF file.

Usage

tiff_torast(path_to_tif)
tiff_torast(path_to_tif)

Arguments

path_to_tif

TIFF file. This is an encoding of map in raster format.

Value

SpatRaster.

Examples


# Generate raster for usage
fp <- paste(tempfile(), ".tif", sep = "")
ret <- utils::download.file(
"https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/avocado_HarvestedAreaFraction.tif",
destfile = fp, method = "auto", mode = "wb")
tiff_torast(fp)

# Generate raster for usage
fp <- paste(tempfile(), ".tif", sep = "")
ret <- utils::download.file(
"https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/avocado_HarvestedAreaFraction.tif",
destfile = fp, method = "auto", mode = "wb")
tiff_torast(fp)

Package 'geohabnet'

Help Index

Internal function to extract risk indices from a list of crop rasters.

Description

Usage

Arguments

Value

Calculate and plot maps

Description

Usage

Arguments

Details

Value

References

See Also

Get raster object for crop

Description

Usage

Arguments

Value

Examples

Get sum of rasters for individual crops

Description

Usage

Arguments

Value

See Also

Examples

Distance methods supported

Description

Usage

Value

Examples

GeoModel class

Description

Slots

GeoNetwork

Description

Usage

Arguments

Value

Slots

GeoRaster class

Description

Fields

Get geographical scales from the parameters

Description

Usage

Arguments

Value

Get Parameters

Description

Usage

Arguments

Details

Value

See Also

Examples

Get rasters object from parameters

Description

Usage

Arguments

Value

See Also

Examples

Global geographical extent

Description

Usage

Details

Value

See Also

GlobalRast class

Description

Fields

Gmap class

Description

Usage

Arguments

Value

Slots