NEWS.md

In neuroconductor/eegUtils: Utilities for Electroencephalographic (EEG) Analysis

eegUtils 0.7.0

Function changes

• Add imax method to run_ICA(). This allows use of the infomax ICA algorithm from the infomax package, which is a reimplementation of the Infomax algorithm used in the EEGLAB Matlab toolbox.
• erp_scalp() and interactive_scalp() should now appropriately use channel locations included in the data.
• More informative messages when using compute_tfr().
• plot_tfr() now applies baseline correction on a single-trial basis where possible, which may show different results when using non-linear baseline correction (e.g. divide or dB)
• topoplot() now allows you to provide multiple component numbers when plotting from an eeg_ICA object, and will automatically produce an appropriately facetted plot.
• topoplot() now has a k parameter to control the smoothing when using method = "gam".
• added additional demo_spatial data from a spatial cueing experiment.
• plot_difference() function added for plotting ERP difference waves. Only currently handles two levels.
• Added hanning taper support for compute_tfr. Note that the scaling factors used for all compute_tfr calculations have been adjusted, so the exact numerical values returned will change. However, this is just a scaling factor - the relative distances between values remained unchanged.
• ar_FASTER() has experimental support for eeg_group objects when those objects are eeg_evoked groups. It does not perform rejection but reports how many times each participants data breaks a threshold for a number of measures.
• import_raw() default participant_id is now changed to NA instead of character(1), to promote better use with eeg_combine().
• eeg_combine() will now refuse to combine objects where participant_id is missing (i.e. is NA), and warn when combining objects with the previous default value "". This is to prevent accidentally treating data from different participants as being from the same participant.
• topoplot() now provides informative messages about the head radius used for plotting. The default calculation of r when using interp_limit = "head" has changed and should now be set at the outermost electrode's position + a 10% buffer. Smaller r can be set manually.
• added get_participant_id, set_participant_id, get_recording and set_recording to interact with the epochs metadata in each eegUtils object.
• eeg_combine() handles eeg_tfr() objects better, now returns an error when trying to combine single-trial data.
• plot_timecourse() now handles eeg_tfr() objects.

Internal changes / bug fixes

• erp_scalp() and interactive_scalp() now use cleaner evaluation of the colour argument using rlang
• Fixed adding CSD as new reference when using compute_csd()
• When using a scaling number of cycles in compute_tfr(), they will now also use the spacing parameter to determine log or linear scaling.
• Fixed bug with eeg_average() used on c("eeg_group", "eeg_tfr") objects.
• Fixed bug with incorrect number of epochs calculated when epoching eeg_data objects if there were multiple "target" triggers appearing in an epoch.
• Fixed error with erp_raster() when anat_order == FALSE
• new epoch_queries file for functions for setting and getting the epochs structure
• new check_items file for functions that check for consistency of various structures
• eeg_combine() with eeg_tfr() no longer drops single dimensions, which was causing issues when there was only one channel or epoch in the object.
• plot_timecourse.eeg_tfr now correctly passes baseline period to rm_baseline()
• filter.eeg_tfr() was sometimes dropping single dimensions when using abind::asub(), now fixed

eegUtils 0.6.3

Function changes

• Added log spaced frequencies to compute_tfr(), with the new spacing argument. plot_tfr automatically detects the spacing and plots the figure appropriately.
• Added na.rm option to erp_image() to either keep or plot trials with NA values due to smoothing. By default they'll be removed.
• Added more informative messages for compute_psd().

Internal changes / bug fixes

• Some minor documentation fixes.
• plot_tfr() error when selecting a specific frequency range fixed.
• Switched to new style of vdiffr tests
• fixed erp_image() smoothing over time instead of epochs.

eegUtils 0.6.2

Function changes

• added support for EEGLAB .set files saved in newer Matlab file formats.
• changed first argument of eeg_filter() to data instead of .data
• added some more informative user messages for importing data and adding electrode locations.
• erp_image() now supports eeg_tfr objects.

Internal changes / bug fixes

• When combining three or more continuous eeg_data objects, eeg_combine() would substantially undercorrect the timing of events in the third file - this is now fixed.
• groups parameter for topoplot() now correctly passed for all types of object.
• stat_tests.R file removed, will be reimplemented elsewhere
• Long standing issues with import of channel locations from EEGLAB files hopefully fixed...
• rm_baseline() for eeg_evoked no longer uses data.table
• as.data.frame.eeg_evoked() handles grouped data better.
• import_set() now handles all EEGLAB formats better.

eegUtils 0.6.1

Function changes

• ar_eogcor now has a bipolarize argument which can be set to false when the HEOG/VEOG channels are already bipolarized.
• added some new ggplot2 based functions for topoplotting and adding contours
  • stat_scalpcontours()
• geom_topo() now has contours
• added errors with when attempting to use compute_psd or compute_tfr on eeg_group objects.
• compute_tfr() now works better with eeg_evoked objects that contain multiple conditions.

Internal changes / bug fixes

• eeg_reference now handles multiple reference channels better on rereferencing
• get_scalpmap handles eeg_ICA components better when there are channels with no locations
• Travis-CI removed.
• cart_to_spherical coord flipping bug fixed (hopefully...)
• filter now converts to tibble internally and does not coerce signals to a vector when there is only one channel.
• added copyright info to summary_contour file
• eeg_combine.eeg_evoked made to behave more consistently when creating grouped data
• all as.data.frame() functions moved to df_converters.r

eegUtils 0.6.0

IMPORTANT: There have been some changes to the logic of the topoplot() that may make their appearance quite different. Specifically, these changes are to the way the underlying interpolation grid is calculated and to how things like the diameter of the cartoon head is calculated. These changes often lead to different minimum or maximum amplitudes across the image, and thus changes in the appearance of the plot due to different scales- don't be alarmed!

Function changes

• epoch_data baseline correction now defaults to no baseline correction
• Added filter method for eeg_tfr objects
• fit_glm() overhauled. Now far faster and allows specification of models using standard R formulae.
• New eeg_lm class introduced for output of fit_glm().
• plot_butterfly.eeg_lm() method added
• as.data.frame() methods have been added for eeg_lm objects.
• view_ica() Shiny viewer for eeg_ICA and eeg_decomp objects added.
• view_artefacts()Shiny viewer for channel and epoch stats added.
• plot_timecourse() now takes a mapping argument, which allows use of ggplot2 aes() mappings
• eeg_average.eeg_tfr() now follows behaviour of other eeg_average() methods in respecting the epochs structure.
• compute_itc() added for computing inter-trial coherence from eeg_tfr objects.
• cols added to eeg_average.eeg_tfr
• eeg_combine.tfr_average() added to handle pre-averaged eeg_tfr objects
• compute_tfr() now allows non-constant number of cycles
• compute_tfr() now uses a different scaling factor, so raw units should now be microvolts-squared.
• added import_erplab() function
• plot_timecourse() now allows CIs for eeg_group objects.

Internal changes / bug fixes

• plot_tfr() now always drops NA/NaN values and averages appropriately over electrodes and conditions.
• import_set() handles continuous EEG data from EEGLAB much better
• Now using whitening package for whitening before SOBI ICA
• select_epochs for eeg_ICA objects fixed to correctly remove epochs from signals
• added tests for filter.eeg_ICA and filter.eeg_tfr
• fixed filter.eeg_data and filter.eeg_evoked
• select_elecs for eeg_ICA now correctly removes components from the unmixing matrix
• switched back to using left_join from dplyr in the tag_events function as an easy fix for sorting of events when tagging.
• fixed odd interaction between select() and validate_channels() that reordered channel names in chan_info
• eeg_decomp now doing better job of filtering for ssd method
• various tibble related warnings and errors cleaned up.
• method = "gam" should now yield sensible results for geom_topo()
• run_ICA() and eeg_decomp() methods now return components ordered by percent variance explained (high to low)
• removed scaling of components in SOBI ICA method
• browse_data().eeg_ica grid res reduced
• eeg_reference().eeg_epochs was always average referencing, now fixed.
• cleaner code in topoplot() for biharmonic smooth
• compute_psd() now demeans individual segments when doing Welch FFT; also no longer errors when only one segment per channel
• eeg_tfr() internal structure modified to keep 4 dimensions even after averaging, for consistency
• stat_summary_by_fill() added to do averaging for raster plots effectively.
• convert_tfr() now properly returns converted data
• import_raw() fix for Brain Vision Analyzer files with date fields in the markers
• added version field to most objects

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 determining 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.

neuroconductor/eegUtils documentation built on Feb. 3, 2023, 5:33 p.m.