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eegutils

An R package for processing and plotting of electroencephalography (EEG) data

https://github.com/craddm/eegutils

Science Score: 54.0%

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Keywords

eeg eeg-analysis eeg-data eeg-signals eeg-signals-processing r rstats
Last synced: 6 months ago · JSON representation ·

Repository

An R package for processing and plotting of electroencephalography (EEG) data

Basic Info
Statistics
  • Stars: 106
  • Watchers: 9
  • Forks: 27
  • Open Issues: 23
  • Releases: 11
Topics
eeg eeg-analysis eeg-data eeg-signals eeg-signals-processing r rstats
Created almost 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Code of conduct Citation Codemeta

README.md

eegUtils

Repo Status Coverage Status R-CMD-check DOI <!-- badges: end -->

Overview

eegUtils is a package for the processing, manipulation, and plotting of EEG data. It includes functions for importing data from a variety of file formats (including Biosemi, Brain Vision Analyzer, and EEGLAB), many of the typical steps in pre-preprocessing (filtering, referencing, artefact rejection), more advanced processing techniques (time-frequency analysis, ICA), and several types of plot that are common in the field (ERP plots, time-frequency plots, topographical scalp maps). Although it uses custom object classes, it is designed such that these are always translatable to standard R data.frames, and thus can be used with any of the myriad packages and methods that support standard R formats.

Installation

The package is very much under active development and is subject to a lot of changes. As such, it is not currently available on CRAN.

Install the latest released version from Github as below.

``` r

install.packages("remotes")

remotes::install_github("craddm/eegUtils") ```

To install the latest development version, install from the develop branch as below.

r remotes::install_github("craddm/eegUtils@develop")

You can also find the package on Neuroconductor - for more information about installing packages from Neuroconductor, see the Neuroconductor installation tutorial

Usage

The following examples show how to use eegUtils to produce a few common plots of EEG data from some simple included example data.

ERP butterfly plots

``` r library(eegUtils)

>

> Attaching package: 'eegUtils'

> The following object is masked from 'package:stats':

>

> filter

plotbutterfly(demoepochs) ```

<!-- -->

Topographical plots

``` r topoplot(demoepochs, timelim = c(.22, .25 ))

> Using electrode locations from data.

> Plotting head r 95 mm

```

<!-- -->

Power spectral density

``` r plotpsd(demoepochs)

> Removing channel means per epoch...

> Computing Power Spectral Density using Welch's method.

> FFT length: 256

> Segment length: 84

> Overlapping points: 42 (50% overlap)

```

<!-- -->

Time-frequency analysis

``` r plottfr(computetfr(demoepochs, foi = c(4, 30), nfreq = 20, n_cycles = 3))

> Computing TFR using Morlet wavelet convolution

> Output frequencies using linear spacing: 4 5.37 6.74 8.11 9.47 10.84 12.21 13.58 14.95 16.32 17.68 19.05 20.42 21.79 23.16 24.53 25.89 27.26 28.63 30

> Removing channel means per epoch...

> Returning signal averaged over all trials.

```

<!-- -->

There are many potential processing steps that precede the production of plots like these. For more examples of how to import and process data, or import data from other sources, see the eegUtils website!

Contributing

If you have any bug reports or feature requests, please report them using the Github issue tracker.

If you would like to contribute any code, be that anything from a documentation fix to a whole new feature, then please begin by raising an issue before moving on to file a Github pull request.

You can find a guide to how Github issues and pull requests work here.

Code of Conduct

Please note that the eegUtils project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

  • Name: Matt Craddock
  • Login: craddm
  • Kind: user
  • Location: Lincoln/London, UK
  • Company: The Alan Turing Institute

Research Software Engineer

Citation (CITATION.cff) 

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.2.3
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "eegUtils" in publications use:'
type: software
license: MIT
title: 'eegUtils: Utilities for Electroencephalographic (EEG) Analysis'
version: 0.7.0.9000
abstract: EEG processing and visualization tools. Includes import functions for 'BioSemi'
  (.BDF), 'Neuroscan' (.CNT), 'Brain Vision Analyzer' (.VHDR), 'EEGLAB' (.set) and
  'Fieldtrip' (.mat). Many preprocessing functions such as referencing, epoching,
  filtering, and ICA are available. There are a variety of visualizations possible,
  including timecourse and topographical plotting.
authors:
- family-names: Craddock
  given-names: Matt
  email: matt@mattcraddock.com
preferred-citation:
  type: manual
  title: 'eegUtils: Utilities for Electroencephalographic (EEG) Analysis'
  authors:
  - family-names: Craddock
    given-names: Matt
    email: matt@mattcraddock.com
  version: 0.7.0.9000
  abstract: EEG processing and visualization tools. Includes import functions for
    'BioSemi' (.BDF), 'Neuroscan' (.CNT), 'Brain Vision Analyzer' (.VHDR), 'EEGLAB'
    (.set) and 'Fieldtrip' (.mat). Many preprocessing functions such as referencing,
    epoching, filtering, and ICA are available. There are a variety of visualizations
    possible, including timecourse and topographical plotting.
  repository-code: https://github.com/craddm/eegUtils
  url: https://craddm.github.io/eegUtils
  date-released: '2022-04-25'
  contact:
  - family-names: Craddock
    given-names: Matt
    email: matt@mattcraddock.com
  keywords:
  - eeg
  - eeg-analysis
  - eeg-data
  - eeg-signals
  - eeg-signals-processing
  - r
  - rstats
  license: MIT
  year: '2022'
repository-code: https://github.com/craddm/eegUtils
url: https://craddm.github.io/eegUtils
date-released: '2022-04-25'
contact:
- family-names: Craddock
  given-names: Matt
  email: matt@mattcraddock.com
keywords:
- eeg
- eeg-analysis
- eeg-data
- eeg-signals
- eeg-signals-processing
- r
- rstats
references:
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@rstudio.com
    orcid: https://orcid.org/0000-0002-5147-4711
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    given-names: Kohske
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    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
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    orcid: https://orcid.org/0000-0002-5125-4188
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    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
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    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  year: '2022'
  url: https://CRAN.R-project.org/package=ggplot2
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2022'
  url: https://CRAN.R-project.org/package=dplyr
  version: '>= 1.0.0'
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
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  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Seidel
    given-names: Dana
  year: '2022'
  url: https://CRAN.R-project.org/package=scales
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
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    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=purrr
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Imports
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    given-names: Winston
    email: winston@rstudio.com
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@rstudio.com
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@rstudio.com
  - family-names: Allen
    given-names: Jeff
    email: jeff@rstudio.com
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2022'
  url: https://CRAN.R-project.org/package=shiny
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Girlich
    given-names: Maximilian
  year: '2022'
  url: https://CRAN.R-project.org/package=tidyr
  version: '>= 1.0.0'
- type: software
  title: miniUI
  abstract: 'miniUI: Shiny UI Widgets for Small Screens'
  notes: Imports
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=miniUI
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  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=rlang
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- type: software
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  abstract: 'MASS: Support Functions and Datasets for Venables and Ripley''s MASS'
  notes: Imports
  authors:
  - family-names: Ripley
    given-names: Brian
    email: ripley@stats.ox.ac.uk
  year: '2022'
  url: https://CRAN.R-project.org/package=MASS
- type: software
  title: signal
  abstract: 'signal: Signal Processing'
  notes: Imports
  authors:
  - family-names: Ligges
    given-names: Uwe
    email: ligges@statistik.tu-dortmund.de
  - family-names: Short
    given-names: Tom
    email: tshort@eprisolutions.com
  - family-names: Kienzle
    given-names: Paul
  year: '2022'
  url: https://CRAN.R-project.org/package=signal
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  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  authors:
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
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  abstract: 'matrixStats: Functions that Apply to Rows and Columns of Matrices (and
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  notes: Imports
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2022'
  url: https://CRAN.R-project.org/package=matrixStats
- type: software
  title: pracma
  abstract: 'pracma: Practical Numerical Math Functions'
  notes: Imports
  authors:
  - family-names: Borchers
    given-names: Hans W.
    email: hwborchers@googlemail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=pracma
- type: software
  title: abind
  abstract: 'abind: Combine Multidimensional Arrays'
  notes: Imports
  authors:
  - family-names: Plate
    given-names: Tony
    email: tplate@acm.org
  - family-names: Heiberger
    given-names: Richard
  year: '2022'
  url: https://CRAN.R-project.org/package=abind
- type: software
  title: plotly
  abstract: 'plotly: Create Interactive Web Graphics via ''plotly.js'''
  notes: Imports
  authors:
  - family-names: Sievert
    given-names: Carson
    email: cpsievert1@gmail.com
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  - family-names: Parmer
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  - family-names: Hocking
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  - family-names: Chamberlain
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  - family-names: Ram
    given-names: Karthik
    email: karthik.ram@gmail.com
  - family-names: Corvellec
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    email: marianne.corvellec@igdore.org
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  - family-names: Despouy
    given-names: Pedro
    email: pedro@plot.ly
  year: '2022'
  url: https://CRAN.R-project.org/package=plotly
- type: software
  title: future.apply
  abstract: 'future.apply: Apply Function to Elements in Parallel using Futures'
  notes: Imports
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2022'
  url: https://CRAN.R-project.org/package=future.apply
- type: software
  title: Rcpp
  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
  - family-names: Francois
    given-names: Romain
  - family-names: Allaire
    given-names: JJ
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  - family-names: Kou
    given-names: Qiang
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    given-names: Nathan
  - family-names: Ucar
    given-names: Inaki
  - family-names: Bates
    given-names: Douglas
  - family-names: Chambers
    given-names: John
  year: '2022'
  url: https://CRAN.R-project.org/package=Rcpp
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  authors:
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  year: '2022'
  url: https://CRAN.R-project.org/package=data.table
- type: software
  title: isoband
  abstract: 'isoband: Generate Isolines and Isobands from Regularly Spaced Elevation
    Grids'
  notes: Imports
  authors:
  - family-names: Wilke
    given-names: Claus O.
    email: wilke@austin.utexas.edu
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2022'
  url: https://CRAN.R-project.org/package=isoband
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
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- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
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- type: software
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  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
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  - family-names: McPherson
    given-names: Jonathan
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  - family-names: Luraschi
    given-names: Javier
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  - family-names: Ushey
    given-names: Kevin
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  - family-names: Atkins
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  - family-names: Wickham
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  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Chang
    given-names: Winston
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  - family-names: Iannone
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- type: software
  title: JADE
  abstract: 'JADE: Blind Source Separation Methods Based on Joint Diagonalization
    and Some BSS Performance Criteria'
  notes: Suggests
  authors:
  - family-names: Nordhausen
    given-names: Klaus
    email: klaus.nordhausen@tuwien.ac.at
    orcid: https://orcid.org/0000-0002-3758-8501
  - family-names: Cardoso
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  abstract: 'whitening: Whitening and High-Dimensional Canonical Correlation Analysis'
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  - family-names: Strimmer
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  - family-names: Jendoubi
    given-names: Takoua
  - family-names: Kessy
    given-names: Agnan
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  abstract: 'ini: Read and Write ''.ini'' Files'
  notes: Suggests
  authors:
  - family-names: Dias
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  year: '2022'
  url: https://CRAN.R-project.org/package=ini
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  abstract: 'mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation'
  notes: Suggests
  authors:
  - family-names: Wood
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    email: simon.wood@r-project.org
  year: '2022'
  url: https://CRAN.R-project.org/package=mgcv
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  abstract: 'infomax: Infomax Independent Component Analysis'
  notes: Suggests
  authors:
  - family-names: Craddock
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  year: '2022'
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  notes: LinkingTo
  authors:
  - family-names: Eddelbuettel
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  - family-names: Bates
    given-names: Doug
  - family-names: Ni
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CodeMeta (codemeta.json) 

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}

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Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
DESCRIPTION cran
  • R >= 3.3.0 depends
  • MASS * imports
  • Matrix * imports
  • Rcpp * imports
  • abind * imports
  • data.table * imports
  • dplyr >= 1.0.0 imports
  • future.apply * imports
  • ggplot2 * imports
  • isoband * imports
  • matrixStats * imports
  • miniUI * imports
  • plotly * imports
  • pracma * imports
  • purrr * imports
  • rlang >= 0.4.0 imports
  • scales * imports
  • shiny * imports
  • signal * imports
  • stats * imports
  • tibble * imports
  • tidyr >= 1.0.0 imports
  • JADE * suggests
  • R.matlab * suggests
  • covr * suggests
  • edfReader * suggests
  • fICA * suggests
  • geigen * suggests
  • hdf5r * suggests
  • ica * suggests
  • infomax >= 0.1.0 suggests
  • ini * suggests
  • knitr * suggests
  • mgcv * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • vdiffr * suggests
  • whitening * suggests
.github/workflows/pkgdown.yaml actions
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  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite