R6 class definition
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
ravepipeline::RAVESerializable -> RAVESubject
@implthe internal object
projectproject instance of current subject; see
RAVEProject
project_namecharacter string of project name
subject_codecharacter string of subject code
subject_idsubject ID: "project/subject"
pathsubject root path
rave_path'rave' directory under subject root path
meta_pathmeta data directory for current subject
imaging_pathroot path to imaging processing folder
freesurfer_path'FreeSurfer' directory for current subject. If
no path exists, values will be NA
preprocess_pathpreprocess directory under subject 'rave' path
data_pathdata directory under subject 'rave' path
cache_pathpath to 'FST' copies under subject 'data' path
pipeline_pathpath to pipeline scripts under subject's folder
report_pathpath to pipeline scripts under subject's folder
note_pathpath that stores 'RAVE' related subject notes
epoch_namespossible epoch names
reference_namespossible reference names
reference_pathreference path under 'rave' folder
preprocess_settingspreprocess instance; see
RAVEPreprocessSettings
blockssubject experiment blocks in current project
electrodesall electrodes, no matter excluded or not
raw_sample_ratesvoltage sample rate
power_sample_ratepower spectrum sample rate
has_waveletwhether electrodes have wavelet transforms
notch_filteredwhether electrodes are Notch-filtered
electrode_typeselectrode signal types
electrode_composedcomposed electrode channels, not actual physically contacts, but is generated from those physically ones
Inherited methods
@marshal()Internal method
RAVESubject$@marshal(...)...internal arguments
@unmarshal()Internal method
RAVESubject$@unmarshal(object, ...)object, ...internal arguments
...ignored
new()constructor
RAVESubject$new(
project_name,
subject_code = NULL,
strict = TRUE,
parent_path = NULL
)project_namecharacter project name
subject_codecharacter subject code
strictwhether to check if subject folders exist
parent_pathparent path if no default path is used, this is for the root directory if subject is in 'BIDS' format
meta_data()get subject meta data located in "meta/" folder
RAVESubject$meta_data(
meta_type = c("electrodes", "frequencies", "time_points", "epoch", "references"),
meta_name = "default",
strict = TRUE
)meta_typechoices are 'electrodes', 'frequencies', 'time_points', 'epoch', 'references'
meta_nameif meta_type='epoch', read in
'epoch_<meta_name>.csv'; if meta_type='references',
read in 'reference_<meta_name>.csv'.
strictwhether to raise errors if the files are missing; default
is true; alternative is to return NULL on missing
valid_electrodes()get valid electrode numbers
RAVESubject$valid_electrodes(reference_name = NULL, refresh = FALSE)reference_namecharacter, reference name, see meta_name
in self$meta_data or load_meta2 when
meta_type is 'reference'
refreshwhether to reload reference table before obtaining data, default is false
initialize_paths()create subject's directories on hard disk
RAVESubject$initialize_paths(include_freesurfer = TRUE)include_freesurferwhether to create 'FreeSurfer' path
set_default()set default key-value pair for the subject, used by 'RAVE' modules
RAVESubject$set_default(key, value, namespace = "default")keycharacter
valuevalue of the key
namespacefile name of the note (without post-fix)
get_default()get default key-value pairs for the subject, used by 'RAVE' modules
RAVESubject$get_default(
...,
default_if_missing = NULL,
simplify = TRUE,
namespace = "default"
)...single key, or a vector of character keys
default_if_missingdefault value is any key is missing
simplifywhether to simplify the results if there is only one key
to fetch; default is TRUE
namespacefile name of the note (without post-fix)
get_note_summary()get summary table of all the key-value pairs used by 'RAVE' modules for the subject
RAVESubject$get_note_summary(namespaces, include_history = FALSE)namespacesnamespaces for the entries; see method
get_default or set_default. Default is all possible
namespaces
include_historywhether to include history entries; default is false
get_epoch()check and get subject's epoch information
RAVESubject$get_epoch(
epoch_name = "default",
as_table = FALSE,
trial_starts = 0
)epoch_nameepoch name, depending on the subject's meta files
as_tablewhether to convert to data.frame; default
is false
trial_startsthe start of the trial relative to epoch time; default is 0
get_reference()check and get subject's reference information
RAVESubject$get_reference(reference_name, simplify = FALSE)reference_namereference name, depending on the subject's meta file settings
simplifywhether to only return the reference column
get_electrode_table()check and get subject's electrode table with electrodes that are load-able
RAVESubject$get_electrode_table(
electrodes,
reference_name,
subset = FALSE,
simplify = FALSE,
warn = TRUE
)electrodescharacters indicating integers such as
"1-14,20-30", or integer vector of electrode numbers
reference_namesee method get_reference
subsetwhether to subset the resulting data table
simplifywhether to only return electrodes
warnwhether to warn about missing electrodes; default is true
get_frequency()check and get subject's frequency table, time-frequency decomposition is needed.
RAVESubject$get_frequency(simplify = TRUE)simplifywhether to simplify as vector
list_pipelines()list saved pipelines
RAVESubject$list_pipelines(
pipeline_name,
cache = FALSE,
check = TRUE,
all = FALSE
)pipeline_namepipeline ID
cachewhether to use cache registry to speed up
checkwhether to check if the pipelines exist
allwhether to list all pipelines; default is false; pipelines with the same label but older time-stamps will be hidden
load_pipeline()load saved pipeline
RAVESubject$load_pipeline(directory)directorypipeline directory name
clone()The objects of this class are cloneable with this method.
RAVESubject$clone(deep = FALSE)deepWhether to make a deep clone.
load_meta2