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devianceResids()
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Calculate binary outcome deviance residuals using probability predictions |
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Features
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Landscape and host feature (variable) data |
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filterRareCommon()
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Filter rare response variables from the data |
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gfData
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Regression data from Fitzpatrick et al 2014 |
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mrFlashlight()
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mrFlashlight: Wrapper to run multi-response model agnostic interpretable machine learning analyses. |
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mrIMLperformance()
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Wrapper to calculate performance metrics (Mathews correlation coefficient, sensitivity and specificity) for each model for each response variable. |
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mrIMLpredicts()
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Wrapper to generate multi-response predictive models. |
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mrInteractions()
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Wrapper to calculate and plot summed interactions of features across response variables. Based on Greenwell et al 2018 |
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mrPlot_interactions()
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Plots global interactions as well as individual response interaction importance. |
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mrProfileplot()
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mrProfileplot: Wrapper to plot mutlti-response model agnostic profile plots (partial dependences and accumulated local effects). |
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mrVip()
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Wrapper to estimate model-agnostic variable importance for multi-response models. |
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plot_vi()
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Plots global importance (i.e. cumulative importance of all features for all response variables) and individual response importance. |
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readSnpsPed()
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Conversion to single column per locus from plink file via LEA functionality |
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resist_components()
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Calculates resistance components from a list of pairwise resistance surfaces. |
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Responsedata
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Viral single nucleuotide polymorphism (SNP) data. |
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vintTidy()
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vintTidy: Interaction effects for tidymodel objects |
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mrBenchmark()
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Compare and benchmark disease outbreak risk among and within groups |
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mrLocalExplainer()
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Run local explanation methods for individual data points |
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MrIMLconverts()
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Converts MrIML objects into a format suitable for IML R package |
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interpret_Mrvi()
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Plots global importance (i.e. cumulative importance of all features for all response variables) and individual response importance. |
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mrProfile2D()
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Plots multi-response 2D profile plots to help interpret interactions |
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plot_vi_biosecurity()
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Plots global importance (i.e. cumulative importance of all features for all response variables) and individual response importance. |