Analyses- R package scari

Here is the index of articles for our package analyses. Start at “Initialize scari” and work through the subsequent steps to follow the package workflow.

Quantify risk to specific viticultural regions

This section explains how to quantify the risk to specific viticultural regions using scari.

1. Example usage of create_risk_report(), applied to create reports for French Viticultural areas
2. Create risk reports for global countries and provinces
3. Create risk reports for the USA nationally and per state

Step 1: Initialize scari and dependencies

Step 2: Retrieve and tidy input data for MaxEnt

1. Retrieve climatic rasters
2. Retrieve occurrence data

Step 3: Execute SDM modeling pipeline

1. Setup and run global-scale MaxEnt model
2. Run global-scale MaxEnt model
3. Setup regional-scale MaxEnt models
4. Run regional-scale MaxEnt model- invaded range in North America
5. Run regional-scale MaxEnt model- invaded range in Asia
6. Run regional-scale MaxEnt model- native range

Step 4: Ensemble regional-scale SDMs

1. Analyze extrapolation using ExDet and MIC analyses
2. Ensemble regional-scale models using measures of extrapolation and best fit

Step 5: Quantify SLF risk

1. Create suitability maps per model scale
2. Create suitability xy plots for viticultural areas
3. Create suitability xy plots for SLF occurrences
4. Generate and format figures of results

Step 6: Validate model fit

1. Assess biological realism of variable response curves
2. Assess goodness of fit via AUC, TSS and confusion matrices
3. Assess variable importance

Function Workflows

• Function: compute_MaxEnt_summary_statistics()