NEWS.md

In kusumikakd/EEG: A collection of utilities for EEG analysis

eegUtils 0.5.0

Function changes

• Default settings for Infomax ICA changed to be similar to EEGLAB/Fieldtrip.
• Faster reading of bdf implemented. Old behaviour can be retained using fast_bdf = FALSE parameter to import_raw()
• eeg_combine now supports combining lists.
• eeg_reference now supports eeg_epochs and eeg_evoked objects.

Internal changes / bug fixes

• plot_butterfly should now be faster again.
• Much faster reader for BDF implemented.
• eeg_filter added demean parameter so that removing channel/epoch means during filtering is now optional. Defaults to TRUE.
• Added artefact detection options for ICA objects
  • ar_acf() checks for low autocorrelation
  • ar_chanfoc() checks for excessive channel focality (e.g. components that load mostly on one channel)
  • ar_trialfoc() checks for trial focality (components that load mostly on a few trials)
  • ar_eogcor() checks for correlation with EOG channels
• topoplot plotting radius logic altered
• compute_csd now uses eeg_reference rather than reref_eeg
• Unmixing matrix for SSD decompositions fixed.
• compute_tfr reworked to be faster.
• Faster baseline correction implemented using Rcpp.
• Padding now used during compute_tfr, which greatly improves speed/accuracy; units may change but this is a change in scaling factor.
• epoch_data now uses a more robust way of determing time limits/samples to include in each epoch that no longer fails at some combinations of time limit and sampling rate
• eeg_average returns objects of class(eeg_evoked, eeg_epochs)
• Updated R requirement to >= 3.2.0
• Updated rlang requirement to >= 0.4.0
• compute_psd fix for single segment data
• updated use of nest and unnest in keeping with tidyr 1.0.0
• as.data.frame.eeg_tfr() now fixed to output correctly

eegUtils 0.4.0

Function changes

• Behaviour of as.data.frame methods changed.
  • cond_label parameter is deprecated
  • Information from the new epochs structure is now automatically added to the data.frame
• tag_epochs function added for labelling
• run_ICA now includes the fICA package version of fastica, and now supports running PCA before ICA.
• apply_ICA function added to remove ICA components.
• Behaviour of select_times() changed to use exact supplied times rather than finding nearest times in the data.
• Some wrappers around dplyr functions added:
  • select() now works for selecting electrodes from eeg_data and eeg_epochs objects.
  • filter() filters by time points or epochs from eeg_data and eeg_epochs objects.
  • mutate() adds columns to the signals from eeg_data and eeg_epochs objects.
• topoplot() now has a groups parameter that allows the possibility of facetting by event labels.
• more Biosemi montages added
• events() function added to easily access and modify the events structure of all eegUtils objects.
• channels() function added to easily access and modify the chan_info structure of all eegUtils objects.
• epochs() function added to access and modify epochs structure.
• ar_eogreg() function added for removing eye movement activity using regression.
• eeg_filter() function added for a unified method of filtering using either FIR or IIR
  • eeg_filter() supports use of multiple threads/cores through the future package.
  • iir_filt() will be deprecated
• geom_topo() extension for ggplot2 added. Allows plotting of a topographical scalp maps using standard ggplot2 functions.
• Default grid_res for topography related plots increased to 200.

Internal changes / bug fixes

• data.table now used in the following functions internally:
  • reref_eeg()
  • iir_filt()
  • eeg_FASTER()
• reref_eeg() now correctly excludes electrodes as requested.
• iir_filt() now correctly respects epoch boundaries.
• New field epochs added to eeg_data and eeg_epochs objects.
• chan_info changes to make chan_info consistent across systems.
• Corrected scaling factor for PSD
• eeg_combine now checks and fixes eeg_data timing consistency
• eeg_tfr objects now use differently organised underlying matrices.
• eeg_ICA fixed unmixing matrices, which were transposed.

eegUtils 0.3.0

Function changes

• topoplot() now has a scaling parameter to scale the size of any lines or markers drawn on the plot.
• plot_tfr() function now useable, with baseline correction also added.
• rm_baseline() now handles eeg_tfr objects.
• as.data.frame() method added for eeg_tfr objects.
• compute_tfr() function now available for use with Morlet wavelets.
• plot_psd() now allows changing of FFT parameters (e.g. number of FFT points, segment length)
• Data selectors added for eeg_tfr objects (e.g. select_elecs())

Internal changes/ bug fixes

• plot_timecourse() overhauled to be S3 method.
• plot_butterfly() reworked internally to be more efficient
• rm_baseline() simplified internally, reworked to use matrices; split to separate file.
• select_elecs() now works for eeg_evoked objects
• eeg_decomp function in progress for performing SSD analyses
• Various methods added for TFR analyses
• topoplot() improvements internally. Now offers potential for facetting.
• Some dplyr functions implemented internally for some objects.

eegUtils 0.2.1

Function changes

• topoplot() added highlights parameter to allow specific electrodes to be highlighted.
• run_ICA() now offers extended Infomax and Fastica thanks to the ica package
• plotly is now a "suggested" package rather than a dependency
• plot_psd() function added to calculate and plot the PSD for eeg_epochs and eeg_data objects
• plot_tfr() function added to handle eeg_tfr objects.
• erp_image() now works with eeg_ICA objects
• Generic print methods added for eeg_epochs and eeg_data
• compute_tfr() function added to performed TFA on eeg_epochs
• epoch_data() now warns if some events are not found rather than stops. Only stops if no events are found.

Internal changes/ bug fixes

• reref_eeg()
  • correctly excludes multiple named electrodes (i.e. passed as characters rather than numbers), where it previously silently failed.
  • no longer records the reference data in the ref_data field
• tf_morlet recoded to be called internally
• compute_psd()
  • recoded to call welch_fft() in order to support possibility of different FFT methods.
  • now drops the DC component (frequency 0)
• welch_fft() internal function added
• eeg_downsample() now makes sure epoch length is a multiple of the downsampling factor to avoid problems with timing jitter
• erp_image() is now an S3 method
• run_ICA()
  • now returns source activations as a "signals" data frame, with component names
  • now returns correct unmixing matrix
• compute_csd()
• added.
• computation of g-matrix and h-matrix refactored, spherical spline calculation altered accordingly
• compute_tfr()
• added
• eeg_FASTER() now properly selects electrodes and epochs for removal

eegUtils 0.2.0

Function changes

• as.data.frame.eeg_epochs() now has a cond_labels parameter to select epochs with specific events and add the event label as an additional column.
• as.data.frame() methods now drop the sample column.
• as.data.frame.eeg_ICA() now has a cond_labels parameter to select epochs with specific events and add the event label as an additional column.
• reref_eeg() now removes reference channels from the data.
• eeg_FASTER() - FASTER artefact rejection method now (mostly) implemented (experimental).

Internal changes / bug fixes

• plot_butterfly() some dplyr use removed.
• run_ica() refactored SOBI method, JADE dependency removed.
• montage_check() command parses montage info when passed to electrode_locations()
• label_check() added to help parse event labels
• proc_events() added to help parse event labels during select_epochs() calls
• topoplot() now tries to average/select across time/epochs before converting to long data, less memory use
• select_elecs() also removes electrodes from chan_info
• select_epochs() fixed bug where events and timings were inconsistent when using keep = FALSE
• Electrode/channel related functions (other than selection) now moved to channel_management.r
• New default electrode locations (347 locations in the 10-05 layout) provided

eegUtils 0.1.15

Function changes

• eeg_evoked() class introduced to hold ERPS
• eeg_ICA() class introduced to hold ICA decompositions
• eeg_average() function to calculate averages (e.g. ERPs) from eeg_epochs objects
• as.data.frame.eeg_evoked() introduced to handle conversion of eeg_evoked objects to data frames.

Internal changes / bug fixes

• compute_psd() function development, converted to S3method.
• topoplot() properly checks for existing chan_info in eeg_data objects
• plot_timecourse() and plot_butterfly() modified to deal with eeg_evoked objects.
• plot_butterfly() updated to better handle data frames
• topoplot.eeg_ICA() added to make topolots from ICA components
• rm_baseline() reworked as S3 method and to be faster and much less memory intensive.
• plot_butterfly() converted to S3 method.
• Initial commits for addition of Morlet wavelet time-frequency analysis
• Initial commits for statisical comparisons added

eegUtils 0.1.14

Function changes

• eeg_downsample() function added to downsample EEG data by an integer factor.
• tag_events() function added to give labels to event codes.
• list_events() added to display unique event codes and their associated labels.
• select_epochs() now allows selection of epochs by event code or event label.
• erp_raster() - plot ERPs across the scalp as an ERP image
• eeg_combine() - combine multiple eeg_data or eeg_epochs objects into one

Internal changes/ bug fixes

• eeg_epochs() now also handles downsampled data appropriately.
• select_times() no longer leaves "epoch" column in eeg_epochs objects.
• topoplot() now calls a separate function (gam_topo()) to create GAM smooths
• browse_data() major speed-ups, no longer converts to long format until necessary. Converted to S3method.
• interactive_scalp() fixed plotting of individual electrodes

eegUtils 0.1.13

Function changes

• interp_elecs() function to perform spherical spline interpolation of individual electrodes
• eeg_ar_thresh() simple absolute value thresholding added
• plot_electrodes() Produces a 2D or interactive 3D plot of electrode locations

eegUtils 0.1.12

Function changes

• iir_filt() now also filters reference channels
• load_set() command added to load EEGLAB .set files

Internal changes

• Converted select_times() to an S3 generic method
• select_times.eeg_data

• select_times.eeg_epochs

• Converted iir_filt() to an S3 generic method

• iir_filt.eeg_data
• iir_filt.eeg_epochs

eegUtils 0.1.11

• Added a NEWS.md file to track changes to the package.

kusumikakd/EEG documentation built on June 28, 2020, 12:30 a.m.