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Protocols

caret specifications

Information


Unique identifier OMICS_19996
Name caret
Alternative name Classification And REgression Training
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 6.0-80
Requirements
R(≥2.10), dplyr, ggplot2, knitr, MASS, ellipse, fastICA, mgcv, pamr, nnet, e1071, pls, rpart, ipred, randomforest, RANN, proxy, testthat(≥0.9.1), kernlab, pROC, mlbench, superpc, lattice(≥0.20), BradleyTerry2, earth(≥2.2-3), gam(≥ 1.15), klaR, mda, MLmetrics, party(≥0.9-99992), spls, subselect, Cubist
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Max Kun
  • person_outline Max Kuhn

Additional information


https://cran.r-project.org/web/packages/caret/

Publication for Classification And REgression Training

caret citations

 (98)
library_books

Metabolic alterations in urine extracellular vesicles are associated to prostate cancer pathogenesis and progression

2018
J Extracell Vesicles
PMCID: 5944373
PMID: 29760869
DOI: 10.1080/20013078.2018.1470442

[…] ith the log2 Fold Change values and Bonferroni adjusted p-values.All statistical analyses were performed using R software v3.3.2 (R Development Core Team, 2016; http://cran.r-project.org) with stats, caret, psych and OptimalCutpoints package []. Boxplots and volcano plots were generated with ggplot2 R package. Correlations with clinical parameters such as BMI were done with cor.test function in R […]

library_books

Classification driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots

2018
PLoS One
PMCID: 5919381
PMID: 29698533
DOI: 10.1371/journal.pone.0196038

[…] he parental analytes were then ranked by the corresponding median VIP across models for the different encoded analytes, scaled between 0 and 1. The entire procedure was conducted using the R package ‘caret’ []. […]

library_books

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

2018
Nat Commun
PMCID: 5916929
PMID: 29695774
DOI: 10.1038/s41467-018-03766-z

[…] g all groups and one-vs.-rest specification (i.e. UCa vs. non-UCa) using the randomForest R package. The optimal value for the mtry parameter was found using 100 five-fold cross-validations using the caret package (https://cran.r-project.org/web/packages/caret/index.html) train-function and ntree = 1000. Feature importance for both classification tasks were extracted using the importance function […]

call_split

Prediction of Return to original work after an Industrial Accident Using Machine Learning and Comparison of Techniques

2018
PMCID: 5934520
PMID: 29736160
DOI: 10.3346/jkms.2018.33.e144
call_split See protocol

[…] ning model, we transformed and reconstructed the models by excluding unimportant variables and/or tuning hyper-parameters to improve the model's performance with automated process using the R package caret (R Foundation, Vienna, Austria). Variable importance was assessed by visualizing the varImp function of the package.The best models with the highest predictive ability for each technique were se […]

library_books

Gene expression links functional networks across cortex and striatum

2018
Nat Commun
PMCID: 5897339
PMID: 29651138
DOI: 10.1038/s41467-018-03811-x

[…] cortical parcel. Tables  and summarize counts of cortical tissue network assignments for the 7- and 17-network solutions. Results were plotted on inflated surface representations of the cortex using Caret.The coordinates of each striatal sample were referenced to the volumetric 7-network functional striatal atlas of Choi et al. (http://surfer.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi20 […]

library_books

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean

2018
Front Genet
PMCID: 5891612
PMID: 29666630
DOI: 10.3389/fgene.2018.00104

[…] Cross validation was performed in R statistical language using the caret package doing K-fold cross validation (). For feature selection we used the PFAM information available for each of the protein sequences after performing InterproScan. For the cross validation, […]

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