'RAVE' class for base repository

The class is for creating child classes, to instantiate the class, please use prepare_subject_bare0 to create base repository.

See also

prepare_subject_bare0

Super class

ravepipeline::RAVESerializable -> RAVESubjectRepository

Public fields

@restored

internal flag indicating whether the repository is restored from serialization. Repositories restored from serialization will behave differently (slightly) for performance considerations

repository_id

repository identifier, typically generated with random string

quiet

whether to suppress update warning messages, when requested electrodes are not fully processed or excluded

Active bindings

auto_exclude

whether to automatically discard channels that are marked as "excluded" (such as bad channels or channels that should not be analyzed); default is often true

meta_info

list of meta information

needs_update

write-only attribute when subject needs to be reloaded from the disk and reference table needs to be updated, use repo$needs_update <- TRUE

project

project instance, see RAVEProject

subject

subject instance, see RAVESubject

electrode_list

integer vector of electrodes included

electrode_table

the entire electrode table

electrode_signal_types

more accurate name should be "channel" signal types: currently returns 'LFP', 'Auxiliary', or 'Spike', for each channel

electrode_instances

electrode channel instance helpers for loading electrode data

reference_name

name of reference table

reference_table

reference table

references_list

a vector of reference channel names, used together with reference_instances

reference_instances

instances of reference channels, for referencing on the fly, used for electrode_instances

digest_key

a list of repository data used to generate repository signature

signature

signature of the repository, two repositories might share the same signature if their contents are the same (even with different identifiers); generated from digest_key

Methods

Public methods

• RAVESubjectRepository$@get_container()

• RAVESubjectRepository$@marshal()

• RAVESubjectRepository$@unmarshal()

• RAVESubjectRepository$print()

• RAVESubjectRepository$new()

• RAVESubjectRepository$export_matlab()

• RAVESubjectRepository$get_electrode_coordinate()

• RAVESubjectRepository$clone()

Inherited methods

• ravepipeline::RAVESerializable$@compare()

---

RAVESubjectRepository$@get_container()

Internal method, do not use it directly

Usage

RAVESubjectRepository$@get_container()

---

RAVESubjectRepository$@marshal()

Internal method

Usage

RAVESubjectRepository$@marshal(...)

Arguments

...

internal arguments

---

RAVESubjectRepository$@unmarshal()

Internal method

Usage

RAVESubjectRepository$@unmarshal(object, ...)

Arguments

object, ...

internal arguments

---

RAVESubjectRepository$print()

User-friendly print method

Usage

RAVESubjectRepository$print()

---

RAVESubjectRepository$new()

constructor

Usage

RAVESubjectRepository$new(
  subject,
  electrodes = NULL,
  reference_name = NULL,
  ...,
  auto_exclude = TRUE,
  quiet = TRUE,
  repository_id = NULL,
  strict = TRUE,
  .class = NULL
)

Arguments

subject

'RAVE' subject

electrodes

string or integers indicating electrodes to load

reference_name

name of the reference table

...

reserved, currently ignored

auto_exclude

whether to automatically discard bad channels

quiet

see field quiet

repository_id

see field repository_id

strict

whether the mode should be strict; default is true and errors out when subject is missing

.class

internally used, do not set, even if you know what this is

---

RAVESubjectRepository$export_matlab()

Export the repository to 'Matlab' for future analysis

Usage

RAVESubjectRepository$export_matlab(..., verbose = TRUE)

Arguments

...

reserved for child classes

verbose

print progresses

Returns

The root directory where the files are stored.

---

RAVESubjectRepository$get_electrode_coordinate()

Get loaded electrode coordinates by type

Usage

RAVESubjectRepository$get_electrode_coordinate(
  type = "LFP",
  electrodes = KEY_MISSING,
  strict = TRUE
)

Arguments

type

length of one or more, electrode channel (signal) type; see constant SIGNAL_TYPES. Default is 'LFP'

electrodes

electrodes to subset, default is a missing key, which uses all the loaded electrodes to subset

strict

whether the returned table must not be empty; default is true, which will raise errors when no electrode matches

Returns

Filtered table; see load_meta2 with meta type 'electrodes'. Besides the mandatory columns, the returned table also contains 'LabelPrefix', used by YAEL to store surgical labels to group channels by electrode device; 'LeadChannel' (logical) to indicate whether the channel is a leading channel in this group, typically the inner-most channel; and 'ShortLabel' for short electrode label.

---

RAVESubjectRepository$clone()

The objects of this class are cloneable with this method.

Usage

RAVESubjectRepository$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.