Table 1.
The 6 classification methods used were implemented in the program R17; the specific functions (and packages) used are given below as well as the different variable importance methods used for each method.
| Method | R Function (package) | Variable importance measure |
|---|---|---|
| LDA | lda (MASS18) | Magnitude of the scalings of the discriminant functions |
| CLR | clogitL1 (clogitL119) | Standardized regression coefficient magnitude |
| Naive Bayes | naiveBayes (e107120) | KL distance between the conditional distribution of each feature given the target class |
| Both SVMs | ksvm (kernlab21) | 1D sensitivity analysis measure based on average absolute deviation from the median22 |
| RF | ranger (ranger23) | Gini index |
| RPCLR | GetVarImp (RPCLR24) | Average change in out of bag AIC with and without each variable |
Abbreviations: AIC, Akaike information criterion; CLR, conditional logistic regression; KL, Kullback Leibler; LDA, linear discriminant analysis; RF, random forests; RPCLR, random penalized conditional logistic regression; SVM, support vector machines.