Learn R Programming

File IO Package for 'RAVE' Project

'RAVE' is a R project that aims at providing interactive analysis and visualization of intracranial Electroencephalography. Developed by Beauchamp's Lab, supported by NIH 1R24MH117529

This package is part of rave family that provides readers from multiple file formats, including:

  • EDF(+), BrainVision, BIDS-iEEG, Matlab files commonly used by neuroscientists
  • HDF5, common file format used by 'Matlab', 'Python', 'C++', and 'R'
  • FST, a file format that supports GB-level read/write speed

Internally support 'RAVE' format; see wiki page.

Installation

raveio is part of rave. Please install rave directly from the wiki page.

To install raveio alone, simply type R command:

install.packages("raveio")

Citation

Please cite the following paper for publication use:

  • Magnotti, JF, Wang, Z, Beauchamp, MS. RAVE: comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data. NeuroImage, 223, p.117341. (DOI)

Please consider citing the following paper as well:

  • Metzger BA, Magnotti JF, Wang Z, Nesbitt E, Karas PJ, Yoshor D, Beauchamp MS. Responses to Visual Speech in Human Posterior Superior Temporal Gyrus Examined with iEEG Deconvolution. Journal of Neuroscience (DOI)
  • Karas PJ, Magnotti JF, Metzger BA, Zhu LL, Smith KB, Yoshor D, Beauchamp MS. The visual speech head start improves perception and reduces superior temporal cortex responses to auditory speech. eLife 2019;8:e48116 (DOI)

You can type print(citation('raveio'), bibtex = TRUE) to print details.

Copy Link

Version

Install

install.packages('raveio')

Monthly Downloads

197

Version

0.9.0

License

GPL-3

Maintainer

Zhengjia Wang

Last Published

July 16th, 2023

Functions in raveio (0.9.0)

PipelineResult

Pipeline result object
RAVEAbstarctElectrode

Abstract definition of electrode class in RAVE
LFP_reference

Definitions of reference with 'LFP' signal type
PipelineCollections

Connect and schedule pipelines
ECoGTensor

'iEEG/ECoG' Tensor class inherit from Tensor
LazyFST

R6 Class to Load 'fst' Files
LazyH5

Lazy 'HDF5' file loader
PipelineTools

Class definition for pipeline tools
BlackrockFile

Class definition to load data from 'BlackRock' 'Micro-systems' files
LFP_electrode

Definitions of electrode with 'LFP' signal type
as_rave_subject

Get RAVESubject instance from character
RAVESubject

Defines 'RAVE' subject class
RAVEPreprocessSettings

Defines preprocess configurations
RAVEProject

Definition for 'RAVE' project class
as_rave_unit

Convert numeric number into print-friendly format
Tensor

R6 Class for large Tensor (Array) in Hybrid Mode
as_rave_project

Convert character to RAVEProject instance
ants_coreg

Register 'CT' or 'MR' images via 'ANTs'
import_electrode_table

Import electrode table into subject meta folder
get_projects

Get all possible projects in 'RAVE' directory
get_val2

Get value or return default if invalid
auto_process_blackrock

Monitors 'BlackRock' output folder and automatically import data into 'RAVE'
convert_blackrock

Convert 'BlackRock' 'NEV/NSx' files
install_modules

Install 'RAVE' modules
backup_file

Back up and rename the file or directory
dir_create2

Force creating directory with checks
cache_path

Manipulate cached data on the file systems
catgl

Print colored messages
RAVEEpoch

Definition for epoch class
RAVEMetaSubject

Defines 'RAVE' subject class for meta analyses
cmd_run_3dAllineate

External shell commands for 'RAVE'
h5_names

Returns all names contained in 'HDF5' file
load_yaml

mgh_to_nii

Convert 'FreeSurfer' 'mgh' to 'Nifti'
pipeline_settings_get_set

Get or change pipeline input parameter settings
lapply_async

Run lapply in parallel
collapse2

Collapse high-dimensional tensor array
h5_valid

Check whether a 'HDF5' file can be opened for read/write
power_baseline

Calculate power baseline
join_tensors

Join Multiple Tensors into One Tensor
collapse_power

Collapse power array with given analysis cubes
new_electrode

Create new electrode channel instance or a reference signal instance
niftyreg_coreg

Register 'CT' to 'MR' images via 'NiftyReg'
generate_reference

Generate common average reference signal for 'RAVE' subjects
find_path

Try to find path along the root directory
convert-fst

Convert 'fst' files to other formats
is.blank

Check If Input Has Blank String
load_meta2

Load 'RAVE' subject meta data
pipeline_install

Install 'RAVE' pipelines
pipeline_collection

Combine and execute pipelines
load_h5

Lazy Load 'HDF5' File via hdf5r-package
is_on_cran

Check if current session is on 'CRAN'
is_valid_ish

Check if data is close to ``valid"
load_bids_ieeg_header

Read in description files from 'BIDS-iEEG' format
load_fst_or_h5

Function try to load 'fst' arrays, if not found, read 'HDF5' arrays
is.zerolenth

Check If Input Has Zero Length
rave-server

Install and configure 'RAVE' server as background service using shiny-server
rave_directories

Returns a list of 'RAVE' directories
pipeline

Creates 'RAVE' pipeline instance
rave-pipeline

'RAVE' pipeline functions
rave-snippet

'RAVE' code snippets
pipeline-knitr-markdown

Configure 'rmarkdown' files to build 'RAVE' pipelines
rave_command_line_path

Find and execute external command-line tools
rave-raw-validation

Validate raw files in 'rave' directory
prepare_subject_bare0

Prepare 'RAVE' single-subject data
rave_brain

Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE'
rave_export

Export 'RAVE' data
module_registry

'RAVE' module registry
progress_with_logger

Enhanced progress with logger message
read_edf_header

Read 'EDF(+)' or 'BDF(+)' file headers
read_edf_signal

Read 'EDF(+)' or 'BDF(+)' file signals
read-write-fst

Read a 'fst' file
module_add

Add new 'RAVE' (2.0) module to current project
save_json

Save or load R object in 'JSON' format
read_csv_ieeg

Read comma separated value file and ignore headers
safe_write_csv

Save data to comma separated value files with backups
read-brainvision-eeg

Load from 'BrainVision' file
py_nipy_coreg

Register 'CT' to 'MR' images via 'nipy' script
rave_subject_format_conversion

Compatibility support for 'RAVE' 1.0 format
raveio-constants

The constant variables
validate_time_window

Validate time windows to be used
validate_subject

Validate subject data integrity
raveio-option

Set/Get 'raveio' option
rave_import

Import data into 'rave' projects
time_diff2

Calculate time difference in seconds
url_neurosynth

Get 'Neurosynth' website address using 'MNI152' coordinates
reexports

Objects exported from other packages
save_meta2

Function to save meta data to 'RAVE' subject
read_nsx_nev

Read 'BlackRock' event and signal files
read_mat

Read 'Matlab' files
safe_read_csv

Read comma separated value files with given column classes
save_h5

Save objects to 'HDF5' file without trivial checks
voltage_baseline

Calculate voltage baseline
with_future_parallel

Enable parallel computing provided by 'future' package within the context
test_hdspeed

Simple hard disk speed test
save_yaml

Write named list to file