ricardoi / CroplandConnectivity

geohabnet

This package is expanded upon Xing et al (2021). It add capabilities to customize parameter values using functions and see results of cropland connectivity risk index in the form of plots. The goal of geohabnet is to enable users to visualize cropland connectivity risk index using their own parameter values. The risk analysis includes 3 maps -

1. Mean cropland connectivity

2. Difference

3. Variance

Package currently support crops sourced from geodata::monfredaCrops() and geodata::spamCrops(). This analysis produces 3 maps - mean, variance and difference for the crop risk index. There are multiple ways in which functions can be used - generate final outcome and then the intermediate outcomes for more sophisticated use cases. Refer to vignettes. This values are propagated to other functions for performing operations such distance matrix calculation. The values are set in parameters.yaml using and it can be accessed using get_parameters(). See the usage below.

Installation

Package can either be installed from CRAN:

install.packages("geohabnet")
#> Installing package into '/private/var/folders/r5/zggvft9d3yn5kh51wqp78rd00000gn/T/RtmpgAVmQR/temp_libpath15ebc6703a975'
#> (as 'lib' is unspecified)
#> installing the source package 'geohabnet'

or the source version of package can be installed from GitHub with:

if (!require("devtools")) {
  install.packages("devtools")
}
#> Loading required package: devtools
#> Loading required package: usethis

devtools::install_github("GarrettLab/CroplandConnectivity", subdir = "geohabnet")
#> Downloading GitHub repo GarrettLab/CroplandConnectivity@HEAD
#> Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
#>   download from 'https://api.github.com/repos/GarrettLab/CroplandConnectivity/tarball/HEAD' failed

geohabnet Example

library(geohabnet)

param_file <- geohabnet::get_parameters()
#> parameters fetched successfully
# now edit the file
geohabnet::set_parameters(new_params = param_file)
#> [1] TRUE

Run the analysis using -

geohabnet::senstivity_analysis()

parameters.yaml stores the parameter and its values. It can be accessed and set using get_parameters() and set_parameters() respectively. By default risk analysis is run on global index, for which scales are present in global_scales() .

Refer to help using ?geohabnet::fun or help(geohabnet::fun)

Refer to article Analyzing risk index using cropland connectivity for more elaborate description and usages of functions in this package.