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Defines 'RAVE' subject class

Source: R/class005-subject.R
RAVESubject.Rd

R6 class definition

Value

data frame

integer vector of valid electrodes

The same as value

A named list of key-value pairs, or if one key is specified and simplify=TRUE, then only the value will be returned.

A data frame with four columns: 'namespace' for the group name of the entry (entries within the same namespace usually share same module), 'timestamp' for when the entry was registered. 'entry_name' is the name of the entry. If include_history is true, then multiple entries with the same 'entry_name' might appear since the obsolete entries are included. 'entry_value' is the value of the corresponding entry.

If as_table is FALSE, then returns as RAVEEpoch instance; otherwise returns epoch table; will raise errors when file is missing or the epoch is invalid.

If simplify is true, returns a vector of reference electrode names, otherwise returns the whole table; will raise errors when file is missing or the reference is invalid.

If simplify is true, returns a vector of electrodes that are valid (or won't be excluded) under given reference; otherwise returns a table. If subset is true, then the table will be subset and only rows with electrodes to be loaded will be kept.

If simplify is true, returns a vector of frequencies; otherwise returns a table.

A table of pipeline registry

A PipelineTools instance

See also

load_meta2

Super class

ravepipeline::RAVESerializable -> RAVESubject

Active bindings

@impl

the internal object

project

project instance of current subject; see RAVEProject

project_name

character string of project name

subject_code

character string of subject code

subject_id

subject ID: "project/subject"

path

subject root path

rave_path

'rave' directory under subject root path

meta_path

meta data directory for current subject

imaging_path

root path to imaging processing folder

freesurfer_path

'FreeSurfer' directory for current subject. If no path exists, values will be NA

preprocess_path

preprocess directory under subject 'rave' path

data_path

data directory under subject 'rave' path

cache_path

path to 'FST' copies under subject 'data' path

pipeline_path

path to pipeline scripts under subject's folder

report_path

path to pipeline scripts under subject's folder

note_path

path that stores 'RAVE' related subject notes

epoch_names

possible epoch names

reference_names

possible reference names

reference_path

reference path under 'rave' folder

preprocess_settings

preprocess instance; see RAVEPreprocessSettings

blocks

subject experiment blocks in current project

electrodes

all electrodes, no matter excluded or not

raw_sample_rates

voltage sample rate

power_sample_rate

power spectrum sample rate

has_wavelet

whether electrodes have wavelet transforms

notch_filtered

whether electrodes are Notch-filtered

electrode_types

electrode signal types

electrode_composed

composed electrode channels, not actual physically contacts, but is generated from those physically ones

Methods

Public methods

Inherited methods

Method @marshal()

Internal method

Usage

RAVESubject$@marshal(...)

Arguments

...

internal arguments

Method @unmarshal()

Internal method

Usage

RAVESubject$@unmarshal(object, ...)

Arguments

object, ...

internal arguments

Method print()

override print method

Usage

RAVESubject$print(...)

Arguments

...

ignored

Method new()

constructor

Usage

RAVESubject$new(
  project_name,
  subject_code = NULL,
  strict = TRUE,
  parent_path = NULL
)

Arguments

project_name

character project name

subject_code

character subject code

strict

whether to check if subject folders exist

parent_path

parent path if no default path is used, this is for the root directory if subject is in 'BIDS' format

Method meta_data()

get subject meta data located in "meta/" folder

Usage

RAVESubject$meta_data(
  meta_type = c("electrodes", "frequencies", "time_points", "epoch", "references"),
  meta_name = "default",
  strict = TRUE
)

Arguments

meta_type

choices are 'electrodes', 'frequencies', 'time_points', 'epoch', 'references'

meta_name

if meta_type='epoch', read in 'epoch_<meta_name>.csv'; if meta_type='references', read in 'reference_<meta_name>.csv'.

strict

whether to raise errors if the files are missing; default is true; alternative is to return NULL on missing

Method valid_electrodes()

get valid electrode numbers

Usage

RAVESubject$valid_electrodes(reference_name = NULL, refresh = FALSE)

Arguments

reference_name

character, reference name, see meta_name in self$meta_data or load_meta2 when meta_type is 'reference'

refresh

whether to reload reference table before obtaining data, default is false

Method initialize_paths()

create subject's directories on hard disk

Usage

RAVESubject$initialize_paths(include_freesurfer = TRUE)

Arguments

include_freesurfer

whether to create 'FreeSurfer' path

Method set_default()

set default key-value pair for the subject, used by 'RAVE' modules

Usage

RAVESubject$set_default(key, value, namespace = "default")

Arguments

key

character

value

value of the key

namespace

file name of the note (without post-fix)

Method get_default()

get default key-value pairs for the subject, used by 'RAVE' modules

Usage

RAVESubject$get_default(
  ...,
  default_if_missing = NULL,
  simplify = TRUE,
  namespace = "default"
)

Arguments

...

single key, or a vector of character keys

default_if_missing

default value is any key is missing

simplify

whether to simplify the results if there is only one key to fetch; default is TRUE

namespace

file name of the note (without post-fix)

Method get_note_summary()

get summary table of all the key-value pairs used by 'RAVE' modules for the subject

Usage

RAVESubject$get_note_summary(namespaces, include_history = FALSE)

Arguments

namespaces

namespaces for the entries; see method get_default or set_default. Default is all possible namespaces

include_history

whether to include history entries; default is false

Method get_epoch()

check and get subject's epoch information

Usage

RAVESubject$get_epoch(
  epoch_name = "default",
  as_table = FALSE,
  trial_starts = 0
)

Arguments

epoch_name

epoch name, depending on the subject's meta files

as_table

whether to convert to data.frame; default is false

trial_starts

the start of the trial relative to epoch time; default is 0

Method get_reference()

check and get subject's reference information

Usage

RAVESubject$get_reference(reference_name, simplify = FALSE)

Arguments

reference_name

reference name, depending on the subject's meta file settings

simplify

whether to only return the reference column

Method get_electrode_table()

check and get subject's electrode table with electrodes that are load-able

Usage

RAVESubject$get_electrode_table(
  electrodes,
  reference_name,
  subset = FALSE,
  simplify = FALSE,
  warn = TRUE
)

Arguments

electrodes

characters indicating integers such as "1-14,20-30", or integer vector of electrode numbers

reference_name

see method get_reference

subset

whether to subset the resulting data table

simplify

whether to only return electrodes

warn

whether to warn about missing electrodes; default is true

Method get_frequency()

check and get subject's frequency table, time-frequency decomposition is needed.

Usage

RAVESubject$get_frequency(simplify = TRUE)

Arguments

simplify

whether to simplify as vector

Method list_pipelines()

list saved pipelines

Usage

RAVESubject$list_pipelines(
  pipeline_name,
  cache = FALSE,
  check = TRUE,
  all = FALSE
)

Arguments

pipeline_name

pipeline ID

cache

whether to use cache registry to speed up

check

whether to check if the pipelines exist

all

whether to list all pipelines; default is false; pipelines with the same label but older time-stamps will be hidden

Method load_pipeline()

load saved pipeline

Usage

RAVESubject$load_pipeline(directory)

Arguments

directory

pipeline directory name

Method clone()

The objects of this class are cloneable with this method.

Usage

RAVESubject$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.