neuralnetwork

neuralnetwork fits multilayer perceptrons for tabular data in R. It accepts formulas, data frames, matrices, and vectors; handles regression and classification; and includes tuning, cross-validation, metrics, feature importance, and model save/load helpers. It is meant for users who need more than nnet’s single-hidden-layer interface or neuralnet’s manual training style, but do not want to bring in a full deep-learning stack.

Install

install.packages("neuralnetwork")

To install the local source tarball:

install.packages("neuralnetwork_0.1.4.tar.gz", repos = NULL, type = "source")

Quick start

library(neuralnetwork)

fit <- nn_fit(
  Species ~ .,
  data = iris,
  hidden = "auto",
  optimizer = "auto",
  epochs = 20,
  validation_split = 0.2,
  seed = 1,
  verbose = FALSE
)

fit
predict(fit, iris[1:5, ], type = "class")
round(predict(fit, iris[1:5, ], type = "prob"), 3)

ev <- nn_evaluate(fit, iris)
ev

The printed model reports the architecture, optimizer, loss, backend, training length, and the selected checkpoint’s training and validation scores. These scores need not come from the last epoch. Epoch optimizers store their trajectory in fit$history; L-BFGS stores final diagnostics in one row. nn_evaluate() returns the metrics as a named vector and prints a compact confusion matrix for classification.

This call scores all of iris, including the rows used for training. It checks the workflow, not performance on new observations. Use nn_cv() for fold-level estimates, and reserve an untouched test set before tuning for a final score.

Macro precision, recall, and F1 include all fitted classes. A class that is never predicted contributes zero instead of disappearing from the average. Class-wise zero denominators return zero. Balanced accuracy averages recall over classes present in the truth, so it can differ from macro recall when an evaluation set omits a fitted class. See help("neuralnetwork-metrics") for the formulas and a worked example.

Row and class weights remain effective with one-row mini-batches. The data gradient uses the full training-weight sum rather than normalizing each batch by its own weights. Zero-weight training rows are omitted from training, scalers and fitted formula bases. Inputs must still pass encoding checks. Finite gradient clipping selects Adam under optimizer = "auto"; explicit L-BFGS rejects clipping rather than ignoring it.

Regression

For regression, put a numeric response on the left side of the formula. Training can scale the target internally; predictions are returned on the original response scale.

fit_reg <- nn_fit(
  mpg ~ wt + hp + disp,
  data = mtcars,
  hidden = c(8, 4),
  optimizer = "adam",
  epochs = 40,
  batch_size = 8,
  learning_rate = 0.01,
  validation_split = 0.2,
  seed = 2,
  verbose = FALSE
)

predict(fit_reg, mtcars[1:5, ])
nn_evaluate(fit_reg, mtcars)

For regression problems with outliers, use Huber loss:

fit_huber <- nn_fit(
  mpg ~ wt + hp + disp,
  data = mtcars,
  hidden = c(8, 4),
  optimizer = "adam",
  loss = "huber",
  huber_delta = 1,
  epochs = 40,
  batch_size = 8,
  learning_rate = 0.01,
  seed = 3,
  verbose = FALSE
)

Choosing settings

Reasonable first choices:

• hidden = "auto" for a small architecture chosen from the task and input width.
• optimizer = "auto" for L-BFGS on small deterministic problems and Adam when using stochastic features such as dropout or callbacks.
• For L-BFGS fits, epochs is the optimizer iteration limit and printed training length is reported as function evaluations.
• validation_split = 0.2 for validation loss, early stopping, or validation-based tuning.
• metric = "balanced_accuracy" for imbalanced classification, metric = "f1" when the positive class is the focus, and metric = "mae" or metric = "rmse" for regression.
• loss = "huber" for regression data where outliers may dominate squared error.

Tuning and validation

tuned <- nn_tune(
  Species ~ .,
  data = iris,
  grid = list(
    hidden = list(4, c(6, 3)),
    learning_rate = c(0.01, 0.003)
  ),
  metric = "balanced_accuracy",
  epochs = 8,
  validation_split = 0.2,
  seed = 4,
  verbose = FALSE
)

tuned
tuned$best_model

For exploratory grids, error_action = "continue" keeps candidate failures in the results table while ranking the usable fits.

cv <- nn_cv(
  Species ~ .,
  data = iris,
  k = 3,
  metric = "f1",
  hidden = 4,
  epochs = 5,
  seed = 5,
  verbose = FALSE
)

cv

Feature importance

imp <- nn_permutation_importance(
  fit_reg,
  mtcars,
  metric = "mae",
  n_repeats = 3,
  seed = 6
)

imp

Function map

What’s included

• Formula, data frame, matrix, and vector inputs.
• Regression, binary classification, and multiclass classification.
• Multiple hidden layers, including hidden = 0 for no hidden layer.
• Adam, SGD, momentum, Nesterov, RPROP, GRPROP, and L-BFGS optimizers.
• Automatic hidden-layer sizing, activation choice, and optimizer choice.
• Portable Rcpp forward-pass kernels when available.
• Dropout, L2 regularization, gradient clipping, learning-rate decay, validation splits, early stopping, and callbacks.
• Sample weights and balanced class weights.
• Huber loss for robust regression.
• Accuracy, balanced accuracy, macro F1, log loss, RMSE, MAE, and R-squared.
• Tuning, repeated k-fold cross-validation, permutation importance, save/load helpers, and S3 predict(), print(), plot(), summary(), and coef().
• Training history plus optimizer convergence metadata for inspecting fitted models, including L-BFGS convergence codes from stats::optim().
• Compatibility helpers for common nnet and neuralnet tasks: nn_multinom(), nn_class_ind(), nn_which_is_max(), nn_compute(), nn_generalized_weights(), nn_gwplot(), nn_hessian(), and nn_confint().

Numerical conventions and limits

Evaluation, tuning and cross-validation use the same metric definitions. Tuning candidates share one holdout, and cross-validation splits row weights along with observations. Undefined scores remain visible rather than silently disappearing. Named predictor and outcome columns must match the fitted model. Formula transformations and contrasts are reused at prediction time.

Multi-output RMSE averages over rows and outputs. R-squared pools output variation after centering each column separately; constant truth returns NA. metric = "loss" uses unpenalized fitted data loss, including Huber loss, on the training target scale. It is not an alias for RMSE.

nn_confint() is limited to converged, unweighted, unregularized no-hidden-layer linear or binary logistic L-BFGS fits. It requires the original training data and refuses singular or saturated fits. nn_hessian() is a curvature diagnostic, not an automatic covariance estimator for a hidden-layer network. Input sensitivities describe encoded-feature derivatives, not neuralnet’s log-odds generalized weights. These helpers are not drop-in inferential replacements for every function in nnet or neuralnet.

Run vignette("neuralnetwork") for the longer worked example.

Reference help inside R: ?neuralnetwork, ?neuralnetwork-metrics, ?neuralnetwork-callbacks, and ?neuralnetwork-objects.

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