General

The General tab groups the following Scenario Datasheets::

• Summary
• Pipeline
• Datafeeds

In the SyncroSim UI, the General tab can be accessed by right-clicking on a WISDM Scenario and selecting Properties from the context menu.

Summary

The Summary Datasheet contains general information about the Scenario.

Name

Defines the name of the Scenario. The name of the Scenario can be defined when creating a new Scenario and modified by editing this field. In the SyncroSim UI, the “Name” can also be edited by right-clicking the Scenario on the Library Explorer window and selecting Rename….

Owner

Defines the owner of the Scenario.

Description

Provides a description of the Scenario, including objectives, species names, geographic extent, and other pertinent information to be captured.

Project

Defines the Project to which the Scenario belongs. The Project is the second highest level of organization within the Library Explorer window. It is nested within the Library level, and contains all of the Scenarios. In the SyncroSim UI, the default Project name “Definitions” can be modified by right-clicking the Project on the Library Explorer window, selecting Properties from the context menu, and editing the “Name” field.

Covariates are defined at the Project scope.

Library

Defines the Library to which the Scenario belongs. The Library is the highest level of organization within the Library Explorer window, and contains the Project. In the SyncroSim UI, the Library name can be modified by right-clicking the Library on the Library Explorer window, selecting Properties from the context menu, and editing the “Name” field .

R and Python configurations are controlled at the Library level.

Last modified

Defines when the Scenario was last modified. It is presented in the following format: Month-Day-Year Hour:Minute:Second AM/PM.

Auto generation tags

Used to autogenerate Scenarios for factorial combinations of parameter inputs.

Read only

Checking “Read only” prevents the Scenario from being edited.

Merge Dependencies

Checking “Merge dependencies” allows the dependencies for the source Scenario(s) to be merged, rather than prioritized. Dependencies allow different steps of the pipeline to be run in different Scenarios. For more information about dependencies, see the SyncroSim documentation.

Ignore Dependencies…

Selecting “Ignore Dependencies” will lead to a panel showing Datafeeds and Packages. Checking the box “Ignore” allows the Scenario to ignore the selected Package(s) when running.

Pipeline

The Pipeline Datasheet is a SyncroSim Core Datasheet that controls which model transformers to run and their run order. For more details, see Scenario Pipeline.

Stage

Defines the transformers that will be run in the Scenario. The general stages in WISDM include:

1. Prepare Multiprocessing
2. Spatial Data Preparation
3. Site Data Preparation
4. Background Data Generation
5. Prepare Training/Testing Data
6. Variable Reduction
7. Models
   • Generalized Linear Model (GLM)
   • Boosted Regression Trees (BRTs): New transformer for building BRT models using methods and defaults described in Valavi et al., 2021. See Appendix 2 for code and model development details.
   • Random Forest
   • Maxent
8. Apply Model
9. Ensemble Model

Here are some short descriptions of each stage:

1. Prepare Multiprocessing: Generates a tiling raster that will be used by subsequent transformers to divide spatial data into smaller chunks for parallel processing. Required inputs: Template Raster File. Outputs: Spatial Multiprocessing Tiling Raster.
2. Spatial Data Preparation: Prepares Covariate and Restriction rasters to align with the extent, resolution, and reference system of the Template raster. Required inputs: Template Raster File, Covariate data. Outputs: Updated covariate data
3. Site Data Preparation: Field Data are projected and clipped to the resolution and extent of the Template Raster. If Aggregate or Weight is selected under Field Data Options, the field data records are aggregated or weighted based on their spatial distribution. Covariate values are then extracted for the remaining field data records. Required inputs: Template Raster File, Field Data, Covariate Data. Outputs: Updated Field Data and Site Data.
4. Background Data Generation: Generates background sites (pseudoabsences), extracts covariate data for the pseudoabsence sites and updates the Field Data and Site Data to include pseudoabsence data. Required inputs: Template Raster File, Field Data, Covariate Data, Site Data. Outputs: Updated Field Data and updated Site Data.
5. Prepare Training/Testing Data: Divides Field Data into training and testing sets and/or cross validation folds based on the provided Validation Options arguments. Required inputs: Field Data, Site Data. Outputs: Updated Field Data.
6. Variable Reduction: Reduces correlated covariates through either an automated approach (using Variance Inflation Factors) or an interactive approach which involves user selection of covariates through a correlation viewer application. Required inputs: Field Data, Site Data. Outputs: Updated Retained Covariate List and a Covariate Selection Matrix if the interactive approach was used.
7. Fit Models (Boosted Regression Trees, Generalized Linear Model, Maxent, Random Forest): Fits the selected model and generates validation and diagnostic summaries and figures. Required inputs: Field Data, Validation Options, Site Data, Retained Covariate List. Outputs: Updated Model Outputs.
8. Apply Model: Generates map outputs for the selected model(s). Maps are generated based on the model, selected Output Options, and the provided Covariate Data. Required inputs: Template Raster File, Model Outputs, Covariate Data. Outputs: Map Outputs
9. Ensemble Model: Generates ensembled outputs of the models run in the Scenario. Ensembles are generated based on the fitted models, apply models, and selected Ensemble Options. Required inputs: Model Outputs, Map Outputs. Outputs: Ensemble Outputs.

Run Order

Sets the order in which the stages will be run.

Jobs

Not currently used by WISDM. Within SyncroSim, it sets the maximum number of jobs per stage. Within WISDM, the number of jobs is defined by the number of multiprocessing tiles.

Datafeeds

The Datafeeds Datasheet summarizes all the Datafeeds parameterized for the Scenario.

Data

Determines whether a given Datasheet has been parameterized. When a new Scenario is created, the “Data” field will be blank, as no data or information has been provided yet. Once a Datasheet has been parameterized, the “Data” field will be set to True and in the SyncroSim UI, a green checkmark will appear.

Package Name

Defines to which Package a given Datasheet belongs. For WISDM models, three Package names will be displayed: “wisdm”, “corestime”, and “core”.

View

Displays the Datasheet and Datafeed names. In the SyncroSim UI, the name will be displayed as a hyperlink that leads to the respective Datasheet.

Datafeed

Defines the names of each Datafeed in the Scenario. In WISDM, the Datasheets and their respective Datafeeds include:

• General - Pipeline
  • Pipeline
• Data Preparation - Spatial Data
  • Template Raster
  • Covariate Data
  • Restriction Raster
• Data Preparation - Field Data
  • Field Data
  • Field Data Options
  • Background Data Options
• Data Preparation - Validation Options
  • Validation Options
• Data Preparation - Spatial Multiprocessing
  • Spatial Multiprocessing
• Variable Reduction
  • Site Data
  • Retained Covariate List
  • Covariate Selection Options
• Models
  • GLM
  • Random Forest
  • Maxent
  • Boosted Regression Tree
  • Model Outputs
• Output Options
  • Output Options
  • Ensemble Options

Source Scenario

Defines the Scenario from which each Datasheet is being drawn.