geohabnet

This package expands on Xing et al (2021)doi:10.1093/biosci/biaa067. It adds capabilities to customize parameter values using functions and shows the results of habitat connectivity risk index in the form of plots. The goal ofgeohabnet is to enable users to visualize a habitat connectivity risk index using their own parameter values. The risk analysis outputs 3 maps -

1. Mean habitat connectivity (based on a habitat connectivity index defined by the user)

2. Difference in habitat connectivity

3. Variance in habitat connectivity

This package currently supports crop maps sourced fromgeodata::monfredaCrops() andgeodata::spamCrops(). This analysis produces the 3 maps listed above. There are multiple ways in which functions can be used - generate the final outcome and then the intermediate outcomes for more sophisticated use cases. The vignettes provide several examples. The output values are propagated to other functions for performing operations such as distance matrix calculation. The values are set inparameters.yaml and it can be accessed usingget_parameters(). See the usage below.

install.packages("geohabnet")#> Installing package into '/private/var/folders/r5/zggvft9d3yn5kh51wqp78rd00000gn/T/Rtmpk04dwi/temp_libpath644e7beb8e10'#> (as 'lib' is unspecified)#> Warning: package 'geohabnet' is not available for this version of R#>#> A version of this package for your version of R might be available elsewhere,#> see the ideas at#> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

if(!require("devtools")){install.packages("devtools")}devtools::install_github("GarrettLab/HabitatConnectivity", subdir="geohabnet")

library(geohabnet)param_file<-geohabnet::get_parameters()# now edit the filegeohabnet::set_parameters(new_params=param_file)

geohabnet::sensitivity_analysis()