Package index

All functions

Features

Landscape and host feature (variable) data

MrShapely()

Generate SHAP (SHapley Additive exPlanations) Plots for Multiple Models and Responses

Responsedata

Viral single nucleotide polymorphism (SNP) data

filterRareCommon()

Filter rare response variables from the data

gfData

Regression data from Fitzpatrick et al. 2014

mrBenchmark()

Compare and benchmark disease outbreak risk among and within groups

mrBootstrap()

Bootstrap model predictions

mrCoOccurNet_bootstrap()

Generate a MrIML co-occurrence network

mrFlashlight()

mrFlashlight: Wrapper to run multi-response model agnostic interpretable machine learning analyses.

mrIMLperformance()

Wrapper to calculate performance metrics (Mathews correlation coefficient, sensitivity and specificity) for each model for each response variable.

mrIMLpredicts()

Wrapper to generate multi-response predictive models.

mrInteractions()

Calculate and visualize feature interactions

mrLocalExplainer()

Run local explanation methods for individual data points

mrPD_bootstrap()

Bootstrap Partial Dependence plots

mrPerformancePlot()

Plot Model Performance Comparison

mrPlot_interactions()

Plots global interactions as well as individual response interaction importance.

mrProfileplot()

mrProfileplot: Wrapper to plot mutlti-response model agnostic profile plots (partial dependences and accumulated local effects).

mrvip()

Calculates and helps interpret variable importance for mrIML models.

mr_Covar()

Calculate covariate partial dependencies for mrIML JSDMs (Joint species distirbution models)

readSnpsPed()

Conversion to single column per locus from plink file via LEA functionality

resist_components()

Calculates resistance components from a list of pairwise resistance surfaces.