This function runs machine learning (ML), evaluates the best model, and optionally calculates feature importance using the framework outlined in Topçuoğlu et al. 2020 (doi: 10.1128/mBio.00434-20 ). Required inputs are a dataframe with an outcome variable and other columns as features, as well as the ML method. See vignette('introduction') for more details.

  outcome_colname = NULL,
  hyperparameters = NULL,
  find_feature_importance = FALSE,
  calculate_performance = TRUE,
  kfold = 5,
  cv_times = 100,
  cross_val = NULL,
  training_frac = 0.8,
  perf_metric_function = NULL,
  perf_metric_name = NULL,
  groups = NULL,
  group_partitions = NULL,
  corr_thresh = 1,
  ntree = 1000,
  seed = NA



Dataframe with an outcome variable and other columns as features.


ML method. Options: c("glmnet", "rf", "rpart2", "svmRadial", "xgbTree").

  • glmnet: linear, logistic, or multiclass regression

  • rf: random forest

  • rpart2: decision tree

  • svmRadial: support vector machine

  • xgbTree: xgboost


Column name as a string of the outcome variable (default NULL; the first column will be chosen automatically).


Dataframe of hyperparameters (default NULL; sensible defaults will be chosen automatically).


Run permutation importance (default: FALSE). TRUE is recommended if you would like to identify features important for predicting your outcome, but it is resource-intensive.


Whether to calculate performance metrics (default: TRUE). You might choose to skip this if you do not perform cross-validation during model training.


Fold number for k-fold cross-validation (default: 5).


Number of cross-validation partitions to create (default: 100).


a custom cross-validation scheme from caret::trainControl() (default: NULL, uses kfold cross validation repeated cv_times). kfold and cv_times are ignored if the user provides a custom cross-validation scheme. See the caret::trainControl() docs for information on how to use it.


Fraction of data for training set (default: 0.8). Rows from the dataset will be randomly selected for the training set, and all remaining rows will be used in the testing set. Alternatively, if you provide a vector of integers, these will be used as the row indices for the training set. All remaining rows will be used in the testing set.


Function to calculate the performance metric to be used for cross-validation and test performance. Some functions are provided by caret (see caret::defaultSummary()). Defaults: binary classification = twoClassSummary, multi-class classification = multiClassSummary, regression = defaultSummary.


The column name from the output of the function provided to perf_metric_function that is to be used as the performance metric. Defaults: binary classification = "ROC", multi-class classification = "logLoss", regression = "RMSE".


Vector of groups to keep together when splitting the data into train and test sets. If the number of groups in the training set is larger than kfold, the groups will also be kept together for cross-validation. Length matches the number of rows in the dataset (default: NULL).


Specify how to assign groups to the training and testing partitions (default: NULL). If groups specifies that some samples belong to group "A" and some belong to group "B", then setting group_partitions = list(train = c("A", "B"), test = c("B")) will result in all samples from group "A" being placed in the training set, some samples from "B" also in the training set, and the remaining samples from "B" in the testing set. The partition sizes will be as close to training_frac as possible. If the number of groups in the training set is larger than kfold, the groups will also be kept together for cross-validation.


For feature importance, group correlations above or equal to corr_thresh (range 0 to 1; default: 1).


For random forest, how many trees to use (default: 1000). Note that caret doesn't allow this parameter to be tuned.


Random seed (default: NA). Your results will only be reproducible if you set a seed.


Named list with results:

  • trained_model: Output of caret::train(), including the best model.

  • test_data: Part of the data that was used for testing.

  • performance: Dataframe of performance metrics. The first column is the cross-validation performance metric, and the last two columns are the ML method used and the seed (if one was set), respectively. All other columns are performance metrics calculated on the test data. This contains only one row, so you can easily combine performance dataframes from multiple calls to run_ml() (see vignette("parallel")).

  • feature_importance: If feature importances were calculated, a dataframe where each row is a feature or correlated group. The columns are the performance metric of the permuted data, the difference between the true performance metric and the performance metric of the permuted data (true - permuted), the feature name, the ML method, the performance metric name, and the seed (if provided). For AUC and RMSE, the higher perf_metric_diff is, the more important that feature is for predicting the outcome. For log loss, the lower perf_metric_diff is, the more important that feature is for predicting the outcome.

More details

For more details, please see the vignettes.


Begüm Topçuoğlu,

Zena Lapp,

Kelly Sovacool,


if (FALSE) {

# regression
run_ml(otu_small, "glmnet",
  seed = 2019

# random forest w/ feature importance
run_ml(otu_small, "rf",
  outcome_colname = "dx",
  find_feature_importance = TRUE

# custom cross validation & hyperparameters
run_ml(otu_mini_bin[, 2:11],
  outcome_colname = "Otu00001",
  seed = 2019,
  hyperparameters = list(lambda = c(1e-04), alpha = 0),
  cross_val = caret::trainControl(method = "none"),
  calculate_performance = FALSE