Package: cito 1.1.1

Maximilian Pichler

cito: Building and Training Neural Networks

The 'cito' package provides a user-friendly interface for training and interpreting deep neural networks (DNN). 'cito' simplifies the fitting of DNNs by supporting the familiar formula syntax, hyperparameter tuning under cross-validation, and helps to detect and handle convergence problems. DNNs can be trained on CPU, GPU and MacOS GPUs. In addition, 'cito' has many downstream functionalities such as various explainable AI (xAI) metrics (e.g. variable importance, partial dependence plots, accumulated local effect plots, and effect estimates) to interpret trained DNNs. 'cito' optionally provides confidence intervals (and p-values) for all xAI metrics and predictions. At the same time, 'cito' is computationally efficient because it is based on the deep learning framework 'torch'. The 'torch' package is native to R, so no Python installation or other API is required for this package.

Authors:Christian Amesöder [aut], Maximilian Pichler [aut, cre], Florian Hartig [ctb], Armin Schenk [ctb]

cito_1.1.1.tar.gz
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cito_1.1.1.tgz(r-4.4-any)cito_1.1.1.tgz(r-4.3-any)
cito_1.1.1.tar.gz(r-4.5-noble)cito_1.1.1.tar.gz(r-4.4-noble)
cito_1.1.1.tgz(r-4.4-emscripten)cito_1.1.1.tgz(r-4.3-emscripten)
cito.pdf |cito.html
cito/json (API)
NEWS

# Install 'cito' in R:
install.packages('cito', repos = c('https://citoverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/citoverse/cito/issues

On CRAN:

machine-learningneural-network

9.07 score 37 stars 1 packages 127 scripts 289 downloads 20 exports 50 dependencies

Last updated 1 months agofrom:6d83920958. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winWARNINGNov 09 2024
R-4.5-linuxWARNINGNov 09 2024
R-4.4-winWARNINGNov 09 2024
R-4.4-macWARNINGNov 09 2024
R-4.3-winWARNINGNov 09 2024
R-4.3-macWARNINGNov 09 2024

Exports:ALEanalyze_trainingavgPoolcnnconditionalEffectsconfig_lr_schedulerconfig_optimizerconfig_tuningcontinue_trainingconvcreate_architecturednnelinearmaxPoolmmnmultinomial_log_probPDPtransfertune

Dependencies:abindbackportsbitbit64bootcallrcheckmateclicorocrayondescellipsisfansifilelockfsgluegridExtragtablehmsjpegjsonlitelatticelifecyclelme4magrittrMASSMatrixminqanlmenloptrparabarpillarpkgconfigpngprettyunitsprocessxprogresspsR6rappdirsRcppRcppEigenrlangsafetensorstibbletorchtorchvisionutf8vctrswithr

Advanced: Custom loss functions and prediction intervals

Rendered fromD-Advanced_custom_loss_functions.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-03-05
Started: 2023-09-29

Example: (Multi-) Species distribution models with cito

Rendered fromC-Example_Species_distribution_modeling.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-03-18
Started: 2023-09-29

Introduction to cito

Rendered fromA-Introduction_to_cito.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-03-16
Started: 2023-09-29

Training neural networks

Rendered fromB-Training_neural_networks.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-03-06
Started: 2023-09-29

Readme and manuals

Help Manual

Help pageTopics
Accumulated Local Effect Plot (ALE)ALE ALE.citodnn ALE.citodnnBootstrap
Visualize training of Neural Networkanalyze_training
This function creates an 'avgPool' layer object of class 'citolayer' for use in constructing a Convolutional Neural Network (CNN) architecture. The resulting layer object can be passed to the 'create_architecture' function to define the structure of the network.avgPool
'cito': Building and training neural networkscito-package cito
Train a Convolutional Neural Network (CNN)cnn
Retrieve parameters of a fitted CNN modelcoef.citocnn
Returns list of parameters the neural network model currently has in usecoef.citodnn coef.citodnnBootstrap
Calculate average conditional effectsconditionalEffects conditionalEffects.citodnn conditionalEffects.citodnnBootstrap
Creation of customized learning rate scheduler objectsconfig_lr_scheduler
Creation of customized optimizer objectsconfig_optimizer
Config hyperparameter tuningconfig_tuning
Continues training of a model generated with 'dnn' or 'cnn' for additional epochs.continue_training continue_training.citocnn continue_training.citodnn continue_training.citodnnBootstrap
Create a Convolutional Layer for a CNN Architectureconv
Create a CNN Architecturecreate_architecture
DNNdnn
Embeddingse
list of specials - taken from enum.RfindReTrmClasses
Create a Linear Layer for a CNN Architecturelinear
Create a Maximum Pooling Layer for a CNN ArchitecturemaxPool
Train and evaluate a Multi-Modal Neural Network (MMN) modelmmn
Multinomial log likelihoodmultinomial_log_prob
Partial Dependence Plot (PDP)PDP PDP.citodnn PDP.citodnnBootstrap
Plot method for citoarchitecture objectsplot.citoarchitecture
Plot a fitted CNN modelplot.citocnn
Creates graph plot which gives an overview of the network architecture.plot.citodnn plot.citodnnBootstrap
Predict with a fitted CNN modelpredict.citocnn
Predict from a fitted dnn modelpredict.citodnn predict.citodnnBootstrap
Predict from a fitted mmn modelpredict.citommn
Print method for citoarchitecture objectsprint.citoarchitecture
Print a fitted CNN modelprint.citocnn
Print class citodnnprint.citodnn print.citodnnBootstrap
Print class citommnprint.citommn
Print average conditional effectsprint.conditionalEffects print.conditionalEffectsBootstrap
Print method for class summary.citodnnprint.summary.citodnn print.summary.citodnnBootstrap
Extract Model Residualsresiduals.citodnn
Data Simulation for CNNsimulate_shapes
Summarize a fitted CNN modelsummary.citocnn
Summarize Neural Network of class citodnnsummary.citodnn summary.citodnnBootstrap
Summary citommnsummary.citommn
combine a list of formula terms as a sumsumTerms
Include a Pretrained Model in a CNN Architecturetransfer
Tune hyperparametertune