Package: rave 1.0.3.3

Zhengjia Wang

rave: R Analysis and Visualization of 'ECOG/iEEG' Data

R Analysis and Visualization of 'ECOG/iEEG' Data RAVE provides cross-platform analysis and visualizations for neuroscience 'ECoG/iEEG' data by "just clicking buttons". This package include: (a) pre-processing of 'ECoG/iEEG' raw data into 'HDF5' format (a cross-platform data format that can be used for R, Matlab, Python, Java and C/C++); (b) 'ECoG/iEEG' epoch and visualizations in real time; (c) Users can write customized analysis as R packages and easily insert into RAVE for interactive visualizations. (d) 3D viewers driven by 'WebGL'.

Authors:Zhengjia Wang [cph, aut, cre], John Magnotti [aut], Michael S. Beauchamp [aut, fnd], Beauchamp lab [cph, fnd]

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rave.pdf |rave.html✨
rave/json (API)

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

Peer review:

Bug tracker:https://github.com/beauchamplab/rave/issues

On CRAN:

4.14 score 23 stars 10 scripts 99 exports 169 dependencies

Last updated 5 months agofrom:7aeb4d9236. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:any_subject_loadedarchive_subjectarrange_data_dirarrange_modulesas_subjectattachDefaultDataRepositorybaselinecachecache_inputcatglcheck_dependenciescheck_subjectclear_cacheclear_envclose_tabcreate_local_cachecustomizedUIdecimate_firdefine_initializationdefine_inputdefine_outputdetect_modulesdiagnose_signaldownload_sample_datadownload_subject_dataECoGRepositoryECoGTensorElectrodeelectrode_localizationeval_when_readyExecEnvirexport_diagnose_voltagefake_sessionfinalize_installationget_dirget_moduleget_pathget_projectsget_rave_themeget_subjectsget_valgetDefaultDataRepositorygetDefaultReactiveInputgetDefaultReactiveOutputgetExecEnvirFromContextgetModuleEnvirFromContextimport_electrodesinit_appinit_modulelapply_asynclapply_async3launch_demoLazyFSTLazyH5load_fst_or_h5load_h5load_metaload_modulesload_rave_module_packageload_scriptsmodule_analysis_namesModuleEnvirmount_demo_subjectnotch_channelnotch_filteropen_tabplot_signalsprogresspwelchr_to_py.Subjectrave_brain2rave_checksrave_contextrave_context_genericsrave_failurerave_ignorerave_import_rawdatarave_module_toolsrave_optionsrave_preparerave_preprocessrave_preprocess_toolsrave_versionread_matreload_module_packagesave_h5save_metasave_optionsset_rave_themeshiny_iconsstart_ravestart_rave2start_yaelSubjectsubject_tmpfileTensorto_moduleview_layoutwavelet

Dependencies:abindaskpassbackportsbase64encbase64urlBHbitbit64bitopsbrewbriobslibcachemcallrcheckmateclicliprcodetoolscommonmarkcpp11crayoncredentialscrosstalkcurldata.tabledescdevtoolsdiffobjdigestdipsausdownlitdownloaderDTedfReaderellipsisevaluatefansifastmapfftwtoolsfilearrayfontawesomeformatRfreesurferformatsfsfstfstcorefuturefuture.applygertghgiftigitcredsglobalsgluegsignalhdf5rherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphiniIRdisplayIRkerneljquerylibjsonliteknitrlaterlatticelazyevallifecyclelistenvloggermagrittrMASSMatrixmemoisemimeminiUImultitaperopenssloro.niftiparallellypbdZMQpillarpkgbuildpkgconfigpkgdownpkgfilecachepkgloadpngpracmapraiseprettyunitsprocessxprofvisprogressrpromisespspurrrR.matlabR.methodsS3R.ooR.utilsR6raggrappdirsravedashraveioravetoolsrcmdcheckRcppRcppEigenRcppTOMLremotesreprreticulaterlangrmarkdownRNiftiRNiftyRegroxygen2rprojrootrpymatrstudioapirversionssasssecretbaseservrsessioninfoshidashishinyshinydashboardshinyFilesshinyjsshinyvalidateshinyWidgetssignalsourcetoolsstartupstringistringrsyssystemfontstargetstestthattextshapingthreeBraintibbletidyselecttinytexurlcheckerusethisutf8uuidvctrswaldowaveslimwhiskerwithrxfunxml2xopenxtableyamlzip

Readme and manuals

Help Manual

Help pageTopics
Function to check if data repository has dataany_subject_loaded
Archive Subject into Zipped filearchive_subject
Initialize data repositoryarrange_data_dir
Update (optional), and check validity of modulesarrange_modules
Make new subject object from characteras_subject
Attach subject dataattachDefaultDataRepository
Baseline signalsbaseline
Import Subject "Matlab" File and Create "HDF5" filescache_raw_voltage
Check if default data environment has objectcheck_data_repo
Check and Install RAVE Dependenciescheck_dependencies
Check if epoch file is validcheck_epoch
Complete validity check a RAVE subjectcheck_subject
check subject validity tools (use check_subjects2)check_subjects_old
check subject validity toolscheck_subjects2
Create local cache to speed up loading speedcreate_local_cache
Customized Shiny ElementscustomizedUI
Decimate or Down-sample a Signal using 'FIR' Filtersdecimate_fir
Defines 'RAVE' Module Initialization Defines the global variables for the module. Called along with 'define_input' to define UI initialization actions once a subject is loaded.define_initialization define_initialization.default define_initialization.rave_module_debug define_initialization.rave_running define_initialization.rave_running_local
Defines 'RAVE' Module Inputsdefine_input define_input.default define_input.rave_module_debug define_input.rave_running define_input.rave_running_local
Define 'RAVE' Module Outputdefine_output define_output.default
Check all packages to for new RAVE module packagesdetect_modules
Plot and Inspect Signals in Trace, Periodogram, and Histogramdiagnose_signal
Function to download demo data to data repositorydownload_sample_data
Function to download subjects from internet/localdownload_subject_data
R6 class for 'iEEG/ECoG' data RepositoryECoGRepository
R6 Class for ElectrodeElectrode
Electrode localizationelectrode_localization
Add Function to run once Module is Readyeval_when_ready
Session-based Module Runtime Environment ClassExecEnvir
Export voltage (analog trace) diagnostic plots for each electrodeexport_diagnose_voltage
Fake 'shiny' Session for Debug Purposefake_session
Finalize installationfinalize_installation
Parse 'RAVE' Module Contentsget_content
Get Directories in `RAVE`get_dir
internally used for debugging functionsget_fake_updated_message
Get RAM usageget_mem_usage
Function to find modules in packagesget_module
Safe Way to Access Module Package Files Using Relative Pathget_path
Get RAVE Theme from Package Settingsget_rave_theme
Get all subjects within projectget_subjects
Get Value or Defaultget_val
Get environment where subject data is loadedgetDefaultDataRepository
Get Module Runtime Environment from Current ContextgetExecEnvirFromContext
Get Module Instance from Current ContextgetModuleEnvirFromContext
Import '.csv' files that contain electrode informationimport_electrodes
Initialize main application for debugging purposeinit_app
Initialize 'RAVE' module for debug purposeinit_module
'lapply' using future package in asynchronous waylapply_async lapply_async3
Load local cache for fast importing voltage, power, and phaseload_local_cache
Load subject meta dataload_meta
Load RAVE Modulesload_modules
Function to load RAVE module package with UI toolsload_rave_module_package
Load scripts that cannot put into package R folderload_scripts
Find module analysis namesmodule_analysis_names
R6 'RAVE' Module ClassModuleEnvir
Load Demo Subject According to Package Configuration Filemount_demo_subject mount_demo_subject.rave_module_debug mount_demo_subject.rave_running mount_demo_subject.rave_running_local
Filter line noise out from ECoG channelsnotch_channel
Apply Notch Filter to Analog Trace Datanotch_filter
Plot signals line by lineplot_signals
A wrapper for shiny Progress objectprogress
Plot "Welch" Periodogrampwelch
Convert subject to python objectr_to_py.Subject
Tools to load and view brain in 3D viewerrave_brain2
Check if data is loaded for current modulerave_checks
'RAVE' Context: Read and Set Context of Environmentsrave_context
Create S3 Generics that Respects 'RAVE' Contextrave_context_generics
RAVE Failure Messagerave_failure
Functions for development userave_ignore
Import Raw Signal from Non-standard Formatsrave_import_rawdata
Tools for module writersrave_module_tools
Function to change rave-optionsrave_options
Load Subject and Create 'iEEG/ECoG' Data Environmentrave_prepare
RAVE Preprocess Functionrave_preprocess
Function to create RAVE preprocess toolsrave_preprocess_tools
Get RAVE versionrave_version
Cache R Objects with Different levelscache cache.default cache.rave_running cache.rave_running_local cache_input clear_cache rave-cache
Open/Close a tab in RAVE main applicationclose_tab open_tab rave-tabs
Make 'iElvis' 'mgrid' fileread_mgrid
Reload 'RAVE' module package without restarting 'RStudio'reload_module_package
Save data to "CSV", if file exists, rename old filesafe_write_csv
Function to save meta data to subjectsave_meta
Function to locally save options (deprecated)save_options
Get `shiny' "input" and "output" objects under current contextgetDefaultReactiveInput getDefaultReactiveInput.default getDefaultReactiveInput.rave_module_debug getDefaultReactiveInput.rave_running getDefaultReactiveInput.rave_running_local getDefaultReactiveOutput getDefaultReactiveOutput.default getDefaultReactiveOutput.rave_module_debug getDefaultReactiveOutput.rave_running getDefaultReactiveOutput.rave_running_local session-reactives
Set and Return RAVE themeset_rave_theme
Convert module to objects used in shinyshinirize
Start RAVE main applicationlaunch_demo start_rave start_rave2
Start 'YAEL' electrode localizationstart_yael
R6 Class for 'RAVE' SubjectSubject
Create temp file in subject module foldersubject_tmpfile
Parse 'SUMA' 'spec' filesuma_spec_parse
Parse 'AFNI' 'BRIK/HEAD' filesuma_surface_volume_parse
Parse 'RAVE' Module and Returns Parsed Content in Environmentsto_module
Debug-use only, reload package, mount demo subject, and launch shiny appview_layout
Wavelet Transformation With Phasewavelet
Returns wavelets to be used for wavelet functionwavelet_kernels