startWorkflow {intSDM} | R Documentation |
startWorkflow
: function to commence the integrated species distribution model workflow.
Description
Function to initialize the reproducible workflow using integrated species distribution models. The arguments for this function are used to specify which species and countries are to be studied, as well as how the results of the model should be saved (either as an R object or saved to some directory). This function outputs an R6
object with additional slot functions to help further customize the model specification. See ?species_model
for more details on these functions.
Usage
startWorkflow(
Countries,
Species,
Projection,
Save = TRUE,
Richness = FALSE,
saveOptions = list(projectDirectory = NULL, projectName = NULL),
Quiet = FALSE
)
Arguments
Countries |
A vector of country names to complete the analysis over. If missing, a boundary object (of class |
Species |
A vector of Species names (scientific) to include in the analysis. Names should be given carefully since the names provided will be used to obtain GBIF observations. |
Projection |
The coordinate reference system used in the workflow. |
Save |
Logical argument indicating if the model objects and outputs should be saved as .rds files. Defaults to |
Richness |
Logical option to create maps for each species individually, or create a species richness model. Defaults to |
saveOptions |
A list containing two items: |
Quiet |
Logical argument indicating if the workflow should provide the user messages during the setup and estimation process. Defaults to |
Value
An R6 object of class species_model
. This object contains a collection of slot functions to assist the user in customizing their workflow.
Examples
##Start a workflow without saving objects
workflow <- startWorkflow(Species = 'Fraxinus excelsior',
Projection = "+proj=longlat +ellps=WGS84",
Save = FALSE,
saveOptions = list(projectName = 'example'))