train.model {SIAMCAT} | R Documentation

## Model training

### Description

This function trains the a machine learning model on the training data

### Usage

    train.model(siamcat,
        method = c("lasso", "enet", "ridge", "lasso_ll",
            "ridge_ll", "randomForest"),
        stratify = TRUE, modsel.crit = list("auc"),
        min.nonzero.coeff = 1, param.set = NULL,
        perform.fs = FALSE,
        param.fs = list(thres.fs = 100, method.fs = "AUC", direction='absolute'),
        feature.type='normalized',
        verbose = 1)

### Arguments

`siamcat` | object of class siamcat-class
`method` | string, specifies the type of model to be trained, may be one of these: `c('lasso', 'enet', 'ridge', 'lasso_ll', 'ridge_ll', 'randomForest')`
`stratify` | boolean, should the folds in the internal cross-validation be stratified?, defaults to `TRUE`
`modsel.crit` | list, specifies the model selection criterion during internal cross-validation, may contain these: `c('auc', 'f1', 'acc', 'pr')`, defaults to `list('auc')`
`min.nonzero.coeff` | integer number of minimum nonzero coefficients that should be present in the model (only for `'lasso'`, `'ridge'`, and `'enet'`), defaults to `1`
`param.set` | list, set of extra parameters for mlr run, may contain: `cost` - for lasso_ll and ridge_ll `alpha` - for enet `ntree` and `mtry` - for RandomForrest. Defaults to `NULL`
`perform.fs` | boolean, should feature selection be performed? Defaults to `FALSE`
`param.fs` | list, parameters for the feature selection, must contain: `thres.fs` - threshold for the feature selection, `method.fs` - method for the feature selection, may be `AUC`, `gFC`, or `Wilcoxon` `direction` - for `AUC` and `gFC`, select either the top associated features (independent of the sign of enrichment), the top positively associated featured, or the top negatively associated features, may be `absolute`, `positive`, or `negative`. Will be ignored for `Wilcoxon`. See Details for more information. Defaults to `list(thres.fs=100, method.fs="AUC", direction='absolute')`
`feature.type` | string, on which type of features should the function work? Can be either `"original"`, `"filtered"`, or `"normalized"`. Please only change this paramter if you know what you are doing!
`verbose` | integer, control output: `0` for no output at all, `1` for only information about progress and success, `2` for normal level of information and `3` for full debug information, defaults to `1`

### Details

This functions performs the training of the machine learning model and functions as an interface to the `mlr`-package.

The function expects a siamcat-class-object with a prepared cross-validation (see create.data.split) in the `data_split`-slot of the object. It then trains a model for each fold of the datasplit.

For the machine learning methods that require additional hyperparameters (e.g. `lasso_ll`), the optimal hyperparameters are tuned with the function tuneParams within the `mlr`-package.

The different machine learning methods are implemented as mlr-tasks:

- `'lasso'`, `'enet'`, and `'ridge'` use the `'classif.cvglmnet'` Learner,

- `'lasso_ll'` and `'ridge_ll'` use the `'classif.LiblineaRL1LogReg'` and the `'classif.LiblineaRL2LogReg'` Learners respectively

- `'randomForest'` is implemented via the `'classif.randomForest'` Learner.

The function can also perform feature selection on each individual fold. At the moment, three methods for feature selection are implemented:

- `'AUC'` - computes the Area Under the Receiver Operating Characteristics Curve for each single feature and selects the top `param.fs$thres.fs`, e.g. 100 features

- `'gFC'` - computes the generalized Fold Change (see check.associations) for each feature and likewise selects the top `param.fs$thres.fs`, e.g. 100 features

- `Wilcoxon` - computes the p-Value for each single feature with the Wilcoxon test and selects features with a p-value smaller than `param.fs$thres.fs`

For `AUC` and `gFC`, feature selection can also be directed, that means that the features will be selected either based on the overall association (`absolute` - `gFC` will be converted to absolute values and `AUC` values below `0.5` will be converted by `1 - AUC`), or on associations in a certain direction (`positive` - positive enrichment as measured by positive values of the `gFC` or `AUC` values higher than `0.5` - and reversely for `negative`).

### Value

object of class siamcat-class with added `model_list`

### Examples

    data(siamcat_example)

    # simple working example
    siamcat_example <- train.model(siamcat_example, method='lasso')

[Package SIAMCAT version 1.4.0 Index]