The goal ofintSDM is to assist users in creating areproducible workflow for large-scale integrated species distributionmodels (ISDM). The package does this by providing the tools andfunctions to obtain species’ occurrence data fromGBIF and environmental covariates fromWorldClim, specify thecomponents of an ISDM, estimate the model, and produce useful outputs.The package estimates the ISDM using a Bayesian framework with theintegratednested Laplace approximation method, which is computationallyefficient in comparison to MCMC methods. Furthermore, the package buildswrapper functions aroundinlabruandPointedSDMs,twoR packages designed to simplify modelling spatial processesand integrated species distribution models respectively. As a result,good knowledge of both these packages is required before usingintSDM.
The outputs of the model are objects which are typically useful inspecies distribution modelling analyses. These include: models,predictions, maps of predictions and cross-validation scores. Thedefault ofintSDM is to produce single-species models andoutputs; however the package does also allow multi-species models toassist the user in obtaining estimates of species richness.
You can install the development version of this package fromGitHub with:
#install.packages('devtools')devtools::install_github("PhilipMostert/intSDM")or directly through CRAN:
install.packages('intSDM')The package contains two main functions:startWorkflowwhich initializes the workflow, andsdmWorkflow, whichestimates one of the specified outcomes of the workflow.startWorkflow produces anR6, which has a multitude ofdifferentslot functions to help customize the workflow. Theseinclude:
| Function name | Function use |
|---|---|
.$plot() | Plot data and other objects required for the model. |
.$addStructured() | Add data not available on GBIF. |
.$addMesh() | Create aninla.mesh object. |
.$addGBIF() | Add data from GBIF. |
.$addArea() | Specify sampling domain. |
.$addCovariates() | Add spatial covariates. |
.$crossValidation() | Specify the cross-validation method. |
.$modelOptions() | AddR-INLA,inlabru andPointedSDMsoptions. |
.$specifySpatial() | Add penalizing complexity priors to the spatial effects. |
.$biasFields() | Specify an additional spatial effect for a dataset. |
.$workflowOutput() | Specify the output of the workflow. |
.$specifyPriors() | Specify the priors of the model. |
.$modelFormula | Add a formula for the covariates and bias of the model. |
.$obtainMeta() | Obtain metadata for the occurrence records. |
Documentation and examples for each of these slot functions mayeasily be obtained using.$help().
Examples of the package being used is provided as vignettes withinthe package.