Subject: R6 Class for 'RAVE' Subject

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

R6 Class for 'RAVE' Subject

Description

contains subject meta information after preprocessing.

Public fields

meta

environment stores subject meta data

subject_id

character, subject ID, generated from project name and subject code. For example, project name is "congruency" and subject code is "YAB", then the subject_id="congruency/YAB"

subject_code

identifier for subject

project_name

project name

dirs

stores folder paths for subject data

is_strict

whether preprocess directory is checked when initializing the instance

Active bindings

electrodes

electrode table (read-only)

frequencies

frequency table (read-only)

time_points

time-point table (read-only)

time_excluded

(deprecated) excluded time-point table (read-only)

sample_rate

time-point table (read-only, for compatibility issues)

volt_sample_rate

voltage (trace) sampling rate in Hertz (read-only)

power_sample_rate

power (amplitude) sampling rate in Hertz (read-only)

phase_sample_rate

phase sampling rate in Hertz (read-only)

valid_electrodes

all valid electrodes in current reference scheme (read-only)

id

read-only version of subject ID

Methods

Public methods

• Subject$info()

• Subject$print()

• Subject$finalize()

• Subject$new()

• Subject$preprocess_info()

• Subject$filter_all_electrodes()

• Subject$filter_valid_electrodes()

• Subject$has_bad_time_point()

• Subject$clone()

---

Method info()

print the information of the subject

Usage

Subject$info()

Returns

none

---

Method print()

override of default print method

Usage

Subject$print(...)

Arguments

...

ignored

Returns

default memory address of the environment

---

Method finalize()

called when garbage collected

Usage

Subject$finalize()

---

Method new()

constructor

Usage

Subject$new(project_name, subject_code, reference = NULL, strict = TRUE)

Arguments

project_name

project name

subject_code

subject code

reference

what kind of reference is default for the subject, default is "default", referring to "reference_default.csv" in subject meta folder

strict

whether to check if the raw folder exists

---

Method preprocess_info()

Obtain preprocessing information. This methods is rarely directly called, I wrap up most commonly used fields in other functions

Usage

Subject$preprocess_info(key, default = NULL, customized = FALSE)

Arguments

key

the fields or items store in SubjectInfo2 instance

default

default value if the key is not found

customized

indicates whether the key refers to additional items or fields in SubjectInfo2. Default is false, meaning the key is the fields.

Returns

the preprocess information correspond to the key

---

Method filter_all_electrodes()

filter, and returns existing electrodes

Usage

Subject$filter_all_electrodes(electrodes)

Arguments

electrodes

integer vector

Returns

the electrodes that the subject has, including bad, or invalid electrodes.

---

Method filter_valid_electrodes()

filter, and returns valid electrodes

Usage

Subject$filter_valid_electrodes(electrodes)

Arguments

electrodes

integer vector

Returns

the valid electrodes. Invalid electrodes refers to bad electrodes, or the end of bipolar reference. If "Reference" column is blank in the reference file, then the electrode is invalid.

---

Method has_bad_time_point()

(deprecated) check whether the selected time is excluded

Usage

Subject$has_bad_time_point(block, electrode, start, end)

Arguments

block

block name

electrode

electrode number

start

start time

end

end time

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Subject$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Author(s)

Zhengjia Wang

Examples

## Not run: 

# Load subject, use `strict=FALSE` if not sure the existence of raw files 
subject <- Subject$new(project_name = 'demo', 'YAB', strict = FALSE)

# Filter 1:14 to see which numbers refer to the valid electrodes
subject$filter_valid_electrodes(1:14)
#> [1] 13 14


## End(Not run)

beauchamplab/rave documentation built on Feb. 16, 2025, 8:12 p.m.