Package 'rave'

Description

Function to check if data repository has data

Usage

any_subject_loaded(rave_data = getDefaultDataRepository())

Arguments

Description

Save subject data, including brain imaging files into a zipped file. Notice this function does not guarantee every file is in. Please always double check what's inside.

Usage

archive_subject(
  project_name,
  subject_code,
  include_cache = FALSE,
  include_fs = TRUE,
  include_raw = FALSE,
  save_to = tempdir()
)

Arguments

Description

Initialize data repository

Usage

arrange_data_dir(first_time = FALSE, reset = FALSE)

Arguments

Description

Update (optional), and check validity of modules

Usage

arrange_modules(refresh = FALSE, reset = FALSE, quiet = FALSE)

Arguments

Description

Make new subject object from character

Usage

as_subject(subject, strict = TRUE, reference = "default")

Arguments

Description

Attach subject data

Usage

attachDefaultDataRepository(
  unload = TRUE,
  rave_data = getDefaultDataRepository()
)

Arguments

Description

Baseline signals

Usage

baseline(
  el,
  from,
  to,
  method = "mean",
  unit = "%",
  data_only = FALSE,
  hybrid = TRUE,
  swap_file = tempfile(),
  mem_optimize = TRUE,
  same_dimension = unit %in% c("%", "dB"),
  preop = NULL,
  op,
  data_env = getDefaultDataRepository()
)

Arguments

Description

Import Subject "Matlab" File and Create "HDF5" files

Usage

cache_raw_voltage(project_name, subject_code, blocks, electrodes, ...)

Arguments

Description

Check if default data environment has object

Usage

check_data_repo(
  var = c("subject"),
  any = FALSE,
  data_repo = getDefaultDataRepository()
)

Arguments

Value

Logical TRUE or FALSE indicating the existence of the variables

Description

Check and Install RAVE Dependencies

Usage

check_dependencies(
  update_rave = TRUE,
  restart = TRUE,
  nightly = FALSE,
  demo_data = FALSE,
  ...
)

Arguments

Description

Check if epoch file is valid

Usage

check_epoch(subject, epoch_name)

Arguments

Description

Complete validity check a RAVE subject

Usage

check_subject(subject, stop_on_error = FALSE)

Arguments

Value

None

Description

check subject validity tools (use check_subjects2)

Usage

check_subjects_old(
  project_name,
  subject_code,
  check = TRUE,
  folders = c("Subject Folder", "RAVE Folder", "Preprocessing Folder", "Meta Folder",
    "Channel Folder"),
  preprocess = c("Started Preprocess", "Notch Filter", "Wavelet"),
  Meta = c("Electrode File", "Time point File", "Frequency File", "Epoch File")
)

Arguments

Description

check subject validity tools

Usage

check_subjects2(project_name, subject_code, quiet = FALSE)

Arguments

Description

Create local cache to speed up loading speed

Usage

create_local_cache(project_name, subject_code, epoch, time_range)

Arguments

Description

Customized Shiny Elements

Usage

customizedUI(inputId, width = 12L, ...)

Arguments

Description

Decimate or Down-sample a Signal using FIR Filters

Usage

decimate_fir(x, q, n = 30)

Arguments

Value

Down-sampled signal

Defines 'RAVE' Module Initialization Defines the global variables for the module. Called along with define_input to define UI initialization actions once a subject is loaded.

Description

Defines 'RAVE' Module Initialization Defines the global variables for the module. Called along with define_input to define UI initialization actions once a subject is loaded.

Usage

define_initialization(expr)

## Default S3 method:
define_initialization(expr)

## S3 method for class 'rave_module_debug'
define_initialization(expr)

## S3 method for class 'rave_running'
define_initialization(expr)

## S3 method for class 'rave_running_local'
define_initialization(expr)

Arguments

Value

None

Examples

## Not run: 
# Requires to install R package beauchamplab/ravebuiltins

# Enable debug mode
ravebuiltins::dev_ravebuiltins(reload = FALSE)
# Check data
define_initialization({
  rave_checks('power')
  power <- module_tools$get_power(referenced = TRUE)
})


# Initialize global variables for modules
ravebuiltins::dev_ravebuiltins(reload = FALSE)
define_initialization({
  print(subject$info())
  time_points = preload_info$time_points
})
define_input(
  shiny::sliderInput('time_range', 'Time-Range', min=0, 
                     max=1, value = c(0,1)),
  init_args = c('min', 'max', 'value'),
  init_expr = {
    min = min(time_points)
    max = max(time_points)
    value = c(0, max)
  }
)

## End(Not run)

Description

Defines 'RAVE' Module Inputs

Usage

define_input(
  definition,
  init_args,
  init_expr,
  keyword = "inputId",
  update_level = 2,
  ...
)

## Default S3 method:
define_input(
  definition,
  init_args,
  init_expr,
  keyword = "inputId",
  update_level = 2,
  ...
)

## S3 method for class 'rave_module_debug'
define_input(definition, init_args, init_expr, ...)

## S3 method for class 'rave_running_local'
define_input(
  definition,
  init_args,
  init_expr,
  keyword = "inputId",
  update_level = 2,
  ...
)

## S3 method for class 'rave_running'
define_input(
  definition,
  init_args,
  init_expr,
  keyword = "inputId",
  update_level = 2,
  ...
)

Arguments

Details

This function behaves differently in different contexts. By default, it returns the result of definition. When debugging modules ( "rave_module_debug"), it assigns a variable to the global environment with the variable name defined as input ID. In other contexts it parse the definition and returns a list for 'RAVE' to use internally to compile the module.

If update_level is '0' then the input is defined as manual inputs, which will not trigger re-calculate if changed. If '1' is set, then the input is a render's input, and only update render functions. If '2' is used, then once user change an input, then the whole module is re-calculated.

init_args must be argument names of the definition. Once subject is loaded, init_expr will be evaluated in a local environment, then variables in init_args will be used to update the input widgets.

Value

See details

Description

Define 'RAVE' Module Output

Usage

define_output(
  definition,
  title = "",
  width = 12L,
  order = Inf,
  keyword = "outputId",
  ...
)

## Default S3 method:
define_output(
  definition,
  title = "",
  width = 12L,
  order = Inf,
  keyword = "outputId",
  ...
)

Arguments

Value

In default or debug context, it returns HTML tags, but when 'RAVE' is running, the result will be parse list for internal use.

Description

Check all packages to for new RAVE module packages

Usage

detect_modules(packages, as_module = TRUE, ...)

Arguments

Description

Plot and Inspect Signals in Trace, Periodogram, and Histogram

Usage

diagnose_signal(
  s1,
  s2 = NULL,
  sc = NULL,
  srate,
  name = "",
  try_compress = TRUE,
  max_freq = 300,
  window = ceiling(srate * 2),
  noverlap = window/2,
  std = 3,
  cex = 1.5,
  lwd = 0.5,
  flim = NULL,
  nclass = 100,
  main = "Channel Inspection",
  col = c("black", "red"),
  which = NULL,
  start_time = 0,
  boundary = NULL,
  mar = c(5.2, 5.1, 4.1, 2.1),
  ...
)

Arguments

Examples

library(stats)
time <- seq(0, 100, by = 1/200)
s2 <- sin(2 * pi * 60 * time) + rnorm(length(time))
diagnose_signal(s2, srate = 200)

# Apply notch filter
s1 = notch_filter(s2, 200, 58,62)
diagnose_signal(s1, s2, srate = 200)

Description

Function to download demo data to data repository

Usage

download_sample_data(subject, version = "v0.1.8-beta", ...)

Arguments

Value

Nothing

Description

Function to download subjects from internet/local

Usage

download_subject_data(
  con,
  replace_if_exists = FALSE,
  override_project = NULL,
  override_subject = NULL,
  temp_dir = tempdir(),
  remove_zipfile = TRUE,
  subject_settings = NULL,
  mode = "wb",
  ...
)

Arguments

Details

Each downloaded zip file should have a "subject.yaml" file indicating default project name, subject code, data directory and raw data directory.

If you want to override subject settings, you need to implement your own subject_settings. See examples.

Examples

## Not run: 
# Normal example
download.file(
  'https://s3-us-west-2.amazonaws.com/rave-demo-subject/sfn-demo/data-large.zip',
  destfile = "~/rave_data/data-small.zip", mode = "wb")
download_subject_data(con = "~/rave_data/data-small.zip")

# or the following
# download_subject_data(
# 'https://s3-us-west-2.amazonaws.com/rave-demo-subject/sfn-demo/data-large.zip'
# )

# rename project to demo_junk
download_subject_data(con = "~/rave_data/data-small.zip",
           override_project = 'demo_junk')

# override settings
download_subject_data(
  con = "~/rave_data/data-small.zip",
  subject_settings = list(
    # subject conf
    'demo_project/demo_subject' = list(
      data_dir = 'data 2/data_dir/demo/sub1',
      raw_dir = 'data 2/raw_dir/sub1'
    )
  )
)

## End(Not run)

Description

A repository to keep subject information, including electrode instances, reference information, epoch data, and offers method to epoch data.

Public fields

Methods

Public methods

• ECoGRepository$info()

• ECoGRepository$print()

• ECoGRepository$new()

• ECoGRepository$get_electrode()

• ECoGRepository$load_electrodes()

• ECoGRepository$epoch()

• ECoGRepository$load_reference()

• ECoGRepository$baseline()

Method info()

obtain the information

Usage

ECoGRepository$info(print = TRUE)

Arguments

Returns

character of the information

Method print()

print memory address

Usage

ECoGRepository$print(...)

Arguments

Returns

none

Method new()

constructor

Usage

ECoGRepository$new(subject, reference = "default", autoload = TRUE)

Arguments

Returns

An ECoGRepository instance

Method get_electrode()

get Electrode instances

Usage

ECoGRepository$get_electrode(electrode, name = "raw")

Arguments

Returns

list of environments containing electrode instances

Method load_electrodes()

load electrodes; usually don't need to directly call this method if autoload is true when initializing the repository

Usage

ECoGRepository$load_electrodes(electrodes, reference = "default")

Arguments

Returns

none

Method epoch()

slice the data according to epoch table

Usage

ECoGRepository$epoch(
  epoch_name,
  pre,
  post,
  electrodes = NULL,
  frequency_range = NULL,
  data_type = "power",
  referenced = TRUE,
  func = NULL,
  quiet = FALSE
)

Arguments

Returns

none. However the results are stored in public fields.

Method load_reference()

load references

Usage

ECoGRepository$load_reference(ref_name, electrodes = NULL)

Arguments

Returns

none

Method baseline()

baseline signals (deprecated)

Usage

ECoGRepository$baseline(from, to, electrodes = NULL, print.time = FALSE)

Arguments

Returns

data after baseline. Please use baseline instead

Author(s)

Zhengjia Wang

Examples

## Not run: 

# Two ways to create instances
repo <- ECoGRepository$new('demo/YAB')

subject <- Subject$new(project_name = 'demo', subject_code = 'YAB')
repo <- ECoGRepository$new(subject)

# Create an instance without auto collecting references, only load 
# interesting electrodes
repo <- ECoGRepository$new('demo/YAB', autoload = FALSE)
repo$load_electrodes(c(14,15))

# Create an instance with non-default reference
repo <- ECoGRepository$new('demo/YAB', reference = 'bipolar')

# Epoch data according to epoch file "epoch_YABaOutlier.csv" in meta folder
# epoch_name should be "epoch_(name).csv"
repo$epoch(epoch_name = 'YABaOutlier', pre = 1, post = 2, 
           electrodes = 14, referenced = TRUE, data_type = "power")
repo$power
#> Dimension:  287 x 16 x 301 x 1 
#> - Trial: 1, 2, 3, 4, 5, 6,...
#> - Frequency: 2, 12, 22, 32, 42...
#> - Time: -1, -0.99, -0.98,...
#> - Electrode: 14


## End(Not run)

Description

Stores single electrode or reference signals

Public fields

Active bindings

Methods

Public methods

• Electrode$info()

• Electrode$print()

• Electrode$switch_reference()

• Electrode$referenced()

• Electrode$clean()

• Electrode$new()

• Electrode$epoch()

Method info()

print electrode information

Usage

Electrode$info()

Returns

none

Method print()

overrides default print method

Usage

Electrode$print(...)

Arguments

Returns

none

Method switch_reference()

switch reference (experimental)

Usage

Electrode$switch_reference(new_reference)

Arguments

Returns

none

Method referenced()

get referenced data

Usage

Electrode$referenced(type = "power", ram = TRUE)

Arguments

Returns

If ram is true, then returns a list of matrices. The length of the list equals the number of blocks, and each matrix is frequency by time points. If ram is false, then returns an environment with each element a LazyH5 or LazyFST instance.

Method clean()

remove data from memory

Usage

Electrode$clean(types = c("power", "phase", "volt"), force = FALSE)

Arguments

Returns

none

Method new()

constructor

Usage

Electrode$new(
  subject,
  electrode,
  reference_by = "noref",
  preload = NULL,
  is_reference = FALSE
)

Arguments

Returns

An Electrode instance

Method epoch()

epoch electrode

Usage

Electrode$epoch(
  epoch_name,
  pre,
  post,
  types = c("volt", "power", "phase"),
  raw = FALSE,
  hybrid = TRUE
)

Arguments

Returns

list of data after epoch

Author(s)

Zhengjia Wang

Examples

## Not run: 
# Electrode with no reference
e1 <- Electrode$new('demo/YAB', electrode = 14, reference_by = 'noref')
e1$reference
#> Subject: demo/YAB
#> Electrode: noref (Reference)

# Add Common Average Reference in rave/data/reference/ref_13-63,65-84.h5
e2 <- Electrode$new('demo/YAB', electrode = 14, 
                    reference_by = 'ref_13-63,65-84')

# Electrode with bipolar reference by another electrode
e3 <- Electrode$new('demo/YAB', electrode = 14, reference_by = 'ref_15')

# Alternative way
reference <- Electrode$new('demo/YAB', electrode = 15, is_reference = TRUE)
e4 <- Electrode$new('demo/YAB', electrode = 14, reference_by = reference)

# e3, e4 are the same in scientific meaning. To test it, epoch them
power3 <- e3$epoch('YABaOutlier', 1, 2, 'power', 
                   raw = FALSE, hybrid = FALSE)$power
power4 <- e4$epoch('YABaOutlier', 1, 2, 'power',
                   raw = FALSE, hybrid = TRUE)$power

# Compare e3 and e4, result difference should be 0
range(power3$get_data() - power4$get_data())
#> 0

# With or without hybrid, the size will be different
# No hybrid, totally in memory
lobstr::obj_size(power3)
#> 12 MB
# Hybrid, data is swapped to hard-drive
lobstr::obj_size(power4)
#> 908 kB

## End(Not run)

Description

Electrode localization

Usage

electrode_localization(subject_code, freesurfer_path, ct_path, ...)

Arguments

Value

This function will launch a shiny application.

Description

Usually contains reactive functions that requires shiny reactive context

Usage

eval_when_ready(FUN)

Arguments

Description

where all the module functions are executed. It's rarely created manually, use get_module to create module, run with start_app(m, test.mode=TRUE), and then inspect modules.

Public fields

Active bindings

Methods

Public methods

• ExecEnvir$reload()

• ExecEnvir$finalize()

• ExecEnvir$info()

• ExecEnvir$print()

• ExecEnvir$clean()

• ExecEnvir$new()

• ExecEnvir$reset()

• ExecEnvir$copy()

• ExecEnvir$execute_with()

• ExecEnvir$names()

• ExecEnvir$register_module()

• ExecEnvir$register_context()

• ExecEnvir$rave_inputs()

• ExecEnvir$rave_outputs()

• ExecEnvir$rave_updates()

• ExecEnvir$rave_execute()

• ExecEnvir$set_browser()

• ExecEnvir$generate_input_ui()

• ExecEnvir$generate_output_ui()

• ExecEnvir$is_global()

• ExecEnvir$clone()

Method reload()

(experimental) signal the modules to reload

Usage

ExecEnvir$reload()

Returns

none

Method finalize()

garbage collection

Usage

ExecEnvir$finalize()

Returns

none

Method info()

print variables in different layers (environment)

Usage

ExecEnvir$info()

Returns

none

Method print()

print the memory address

Usage

ExecEnvir$print(...)

Arguments

Returns

memory address

Method clean()

clean the environments to release the resource

Usage

ExecEnvir$clean()

Returns

none

Method new()

constructor

Usage

ExecEnvir$new(session = getDefaultReactiveDomain(), parent_env = NULL)

Arguments

Method reset()

reset the runtime environment, rarely used

Usage

ExecEnvir$reset(inputs)

Arguments

Returns

none

Method copy()

(deprecated) copy the instance locally

Usage

ExecEnvir$copy(
  session_id = "__fake_runtime_env__",
  data_env = getDefaultDataRepository()
)

Arguments

Returns

a copied instance

Method execute_with()

(deprecated) execute module with given parameter

Usage

ExecEnvir$execute_with(param, async = FALSE, plan = NULL)

Arguments

Returns

runtime environment

Method names()

returns names of a list, if names are null, returns blank characters

Usage

ExecEnvir$names(x)

Arguments

Returns

the names of the list

Method register_module()

register ModuleEnvir instance

Usage

ExecEnvir$register_module(module_env)

Arguments

Returns

none

Method register_context()

Register 'RAVE' context for current environment (internally used)

Usage

ExecEnvir$register_context(context = c("rave_running", "rave_running_local"))

Arguments

Returns

None

Method rave_inputs()

parse input components

Usage

ExecEnvir$rave_inputs(
  ...,
  .input_panels = list(),
  .tabsets = list(),
  .env = NULL,
  .manual_inputs = NULL,
  .render_inputs = NULL
)

Arguments

Returns

none

Method rave_outputs()

parse output components

Usage

ExecEnvir$rave_outputs(
  ...,
  .output_tabsets = list(),
  .tabsets = list(),
  .env = NULL
)

Arguments

Returns

none

Method rave_updates()

input initialization when iEEG/ECoG data are imported

Usage

ExecEnvir$rave_updates(..., .env = NULL)

Arguments

Method rave_execute()

parse, and compile to main function

Usage

ExecEnvir$rave_execute(..., auto = TRUE, .env = NULL, async_vars = NULL)

Arguments

Returns

none, but ExecEnvir$execute will be generated.

Method set_browser()

(experimental) cache R expression in browser localStorage

Usage

ExecEnvir$set_browser(expr, session = getDefaultReactiveDomain())

Arguments

Method generate_input_ui()

generate input panels according to parsed rave_inputs

Usage

ExecEnvir$generate_input_ui(sidebar_width = 3L)

Arguments

Returns

HTML tags

Method generate_output_ui()

generate outputs labels according to parsed rave_outputs

Usage

ExecEnvir$generate_output_ui(sidebar_width = 3L)

Arguments

Returns

HTML tags

Method is_global()

(deprecated) check if variable is shared across modules. Please use cache_input instead to get variable values.

Usage

ExecEnvir$is_global(inputId)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

ExecEnvir$clone(deep = FALSE)

Arguments

Author(s)

Zhengjia Wang

Examples

## Not run: 

# Load module
module <- get_module('ravebuiltins', 'power_explorer')

# Create execute environmen
execenv <- module$get_or_new_exec_env()
execenv$info()


## End(Not run)

Description

You must import subject through rave_preprocess() and then run this function

Usage

export_diagnose_voltage(
  subject,
  electrodes,
  blocks,
  save_dir = "./export",
  width = 12,
  height = 7,
  useDingbats = FALSE,
  onefile = TRUE,
  winlen,
  freq_lim,
  nclass = 50,
  fore_col = "black",
  back_col = "grey80",
  ...
)

Arguments

See Also

pdf, diagnose_signal, pwelch

Description

Fake 'shiny' Session for Debug Purpose

Usage

fake_session(rave_id = "__fake_session__", id = NULL)

Arguments

Value

Fake shiny session for debug purpose

Description

download demo data

Usage

finalize_installation(
  packages,
  upgrade = c("ask", "config-only", "always", "never", "data-only"),
  async = FALSE
)

Arguments

Description

Parse 'RAVE' Module Contents

Usage

get_content(content, env, evaluate = TRUE, chunks = FALSE)

Arguments

Details

If "evaluate=TRUE", then the parse code will be evaluated within env and returns a logical value: TRUE means the content has something, otherwise returns FALSE

If "evaluate=FALSE", returns the parsed expression and add attributes about the names of each chunk and whether they are asynchronous

Value

See details.

Description

Get Directories in 'RAVE'

Usage

get_dir(
  subject_code,
  project_name,
  block_num,
  mkdirs = NULL,
  subject_id,
  relative = FALSE
)

Arguments

Description

internally used for debugging functions

Usage

get_fake_updated_message(..., .args = list(), .func = NULL)

Arguments

Description

Get RAM usage

Usage

get_mem_usage(
  modules = list(),
  data_envir = getDefaultDataRepository(),
  session = getDefaultReactiveDomain()
)

Arguments

Description

Function to find modules in packages

Usage

get_module(package, module_id, local = FALSE, ...)

Arguments

Description

Safe Way to Access Module Package Files Using Relative Path

Usage

get_path(..., mustWork = FALSE, is_directory = FALSE)

Arguments

Value

If you are developing the package, get_path returns the absolute file path, otherwise it uses system.file to get the file from package library.

Description

Get RAVE Theme from Package Settings

Arguments

Value

A list contains all palettes found in the packages.

Examples

pal = get_rave_theme('rave', type = c('continuous', 'discrete'), theme='light')
print(pal, plot=TRUE)

pal = get_rave_theme('rave', type = c('continuous', 'discrete'), theme='dark')
print(pal, plot=TRUE)

Description

Get all subjects within project

Usage

get_subjects(project_name, check_subfolders = TRUE, check_rawdata = FALSE)

Arguments

Description

Get Value or Default

Usage

get_val(x, key = NULL, ..., .invalids = c("null", "na"))

Arguments

Description

Get environment where subject data is loaded

Usage

getDefaultDataRepository(
  session = getDefaultReactiveDomain(),
  session_id,
  session_based = NULL
)

Arguments

Description

Get Module Runtime Environment from Current Context

Usage

getExecEnvirFromContext()

Value

An ExecEnvir instance

Description

Get Module Instance from Current Context

Usage

getModuleEnvirFromContext()

Value

An ModuleEnvir instance

Description

The table to import must contains a column 'Electrode' that is consistent with the corresponding subject.

Usage

import_electrodes(path, subject, use_fs = NA, ...)

Arguments

Description

Initialize main application for debugging purpose

Usage

init_app(
  modules = NULL,
  active_module = NULL,
  launch.browser = TRUE,
  theme = "red",
  disable_sidebar = FALSE,
  simplify_header = FALSE,
  ...,
  data_repo = getDefaultDataRepository()
)

Arguments

Description

Initialize 'RAVE' module for debug purpose

Usage

init_module(
  module_id,
  debug = FALSE,
  parse_context = c("rave_running", "rave_running_local")
)

Arguments

See Also

load_rave_module_package

Description

lapply using future package in asynchronous way

Usage

lapply_async(
  x,
  fun,
  ...,
  .ncores = 0,
  .call_back = NULL,
  .packages = NULL,
  .envir = environment(),
  .globals = TRUE,
  .gc = TRUE,
  .as_datatable = FALSE,
  .nrows = 0
)

lapply_async3(
  x,
  fun,
  ...,
  .globals = TRUE,
  .gc = TRUE,
  .callback = NULL,
  .ncores = 0
)

Arguments

Examples

## Not run: 
lapply_async(1:10, function(x){
  Sys.sleep(2) # Run for 1 secs
  Sys.getpid()
}, .ncores = 3, .call_back = function(i){
  cat('Running iteration -', i, '\n')
})

## End(Not run)

Description

Load local cache for fast importing voltage, power, and phase

Usage

load_local_cache(
  project_name,
  subject_code,
  epoch,
  time_range,
  frequency_range = NULL,
  electrodes,
  referenced = FALSE,
  data_type = "voltage"
)

Arguments

Description

Load subject meta data

Usage

load_meta(meta_type, project_name, subject_code, subject_id, meta_name)

Arguments

Description

Load RAVE Modules

Usage

load_modules(legacy = FALSE)

Arguments

Description

called internally by init_module or other module packages

Usage

load_rave_module_package(
  env,
  parse_context = c("rave_module_debug", "rave_running", "rave_running_local")
)

Arguments

Description

Use in comp.R to load scripts that cannot be put into package "R/" folder. Usually the scripts contains shiny reactive values that changes dynamically.

Usage

load_scripts(..., asis = FALSE)

Arguments

Details

This function raises error when running in default contexts, and requires debug mode, or run inside of 'RAVE' instance.

Value

None, but will source, or run whatever code provided.

See Also

rave_context, get_path, quo

Description

Find module analysis names

Usage

module_analysis_names(
  module_id,
  project_name,
  data_env = getDefaultDataRepository()
)

Arguments

Description

contains module data, functions, etc.

Public fields

Methods

Public methods

• ModuleEnvir$info()

• ModuleEnvir$print()

• ModuleEnvir$new()

• ModuleEnvir$get_or_new_exec_env()

• ModuleEnvir$load_script()

• ModuleEnvir$render_ui()

• ModuleEnvir$clean()

Method info()

print module information

Usage

ModuleEnvir$info()

Returns

none

Method print()

print module information and returns memory address

Usage

ModuleEnvir$print(...)

Arguments

Method new()

constructor

Usage

ModuleEnvir$new(
  module_id,
  label_name,
  script_path,
  author = NULL,
  version = "0",
  packages = NULL,
  .script_content = NULL,
  rmd_path = NULL,
  parent_env = globalenv()
)

Arguments

Method get_or_new_exec_env()

get the corresponding ExecEnvir with shiny session

Usage

ModuleEnvir$get_or_new_exec_env(
  session = getDefaultReactiveDomain(),
  ...,
  new = FALSE
)

Arguments

Returns

an ExecEnvir instance associated with current module and given session

Method load_script()

load and compile script into registered ExecEnvir

Usage

ModuleEnvir$load_script(session = getDefaultReactiveDomain())

Arguments

Returns

none

Method render_ui()

generate 'HTML' tags

Usage

ModuleEnvir$render_ui(session = getDefaultReactiveDomain())

Arguments

Returns

'HTML' tags

Method clean()

clean the module environment

Usage

ModuleEnvir$clean(session = getDefaultReactiveDomain(), session_id)

Arguments

Examples

## Not run: 

module <- get_module('ravebuiltins', 'power_explorer')
module
#> Module Name: Power Explorer 
#> Version: 0 
#> Script Path: ... 
#> Author(s):


## End(Not run)

Description

Load Demo Subject According to Package Configuration File

Usage

mount_demo_subject(
  subject_code,
  project_name,
  force_reload_subject = FALSE,
  ...,
  download_url
)

## S3 method for class 'rave_module_debug'
mount_demo_subject(
  subject_code,
  project_name,
  force_reload_subject = FALSE,
  ...,
  download_url
)

## S3 method for class 'rave_running'
mount_demo_subject(...)

## S3 method for class 'rave_running_local'
mount_demo_subject(...)

Arguments

Details

When debugging the 'RAVE' modules, it loads demo subject for debugging from according to settings file "inst/rave.yaml".

This function only function properly in 'rave_module_debug' mode. This means by default it raises errors. In other mode, for example 'rave_running', it does nothing.

Value

None

Description

Filter line noise out from ECoG channels

Usage

notch_channel(s, sample_rate, bands = c(60, 120, 180), width = c(1, 2, 2))

Arguments

Description

Apply Notch Filter to Analog Trace Data

Usage

notch_filter(s, sample_rate, lb, ub, domain = 1)

Arguments

Details

This function is alternative R version of notch filter

Value

filtered signal in time domain

Description

Plot signals line by line

Usage

plot_signals(
  signals,
  sample_rate = 1,
  col = 1,
  space = 0.995,
  space_mode = "quantile",
  start_time = 0,
  duration = NULL,
  compress = TRUE,
  channel_names = NULL,
  ylab = "Channel",
  time_shift = 0,
  lwd = 0.5,
  cex = 2,
  new_plot = TRUE,
  plot = "base",
  xlim = NULL,
  ...
)

Arguments

Description

A wrapper for shiny Progress object

Usage

progress(
  title,
  max = 1,
  session = getDefaultReactiveDomain(),
  quiet = FALSE,
  ...
)

Arguments

Details

shiny::Progress class cannot be used under non-reactive environment. rave::progress function wrap it up so that you can use it in non-reactive settings.

Description

Plot "Welch" Periodogram

Usage

pwelch(
  x,
  fs,
  window = 64,
  noverlap = 8,
  nfft = 256,
  col = "black",
  xlim = NULL,
  ylim = NULL,
  main = "Welch periodogram",
  plot = TRUE,
  log = "xy",
  spec_func = stats::spectrum,
  cex = 1,
  ...
)

Arguments

Description

Convert subject to python object

Usage

r_to_py.Subject(obj, convert = FALSE)

Arguments

Description

Tools to load and view brain in 3D viewer

Usage

rave_brain2(
  subject,
  surfaces = "pial",
  use_141 = TRUE,
  recache = FALSE,
  clean_before_cache = FALSE,
  compute_template = FALSE,
  usetemplateifmissing = FALSE
)

Arguments

Description

Check if data is loaded for current module

Usage

rave_checks(
  ...,
  data = NULL,
  .raise_error = TRUE,
  rave_data = getDefaultDataRepository()
)

Arguments

Details

This function checks whether "ECoG" data is loaded. The format is: "DATA+(blankspace)+TYPE". "DATA" can be "power" (wavelet transform amplitude), "phase" (complex angle), or "volt"/"voltage" (Before wavelet). "TYPE" can be "raw" (no reference), "referenced" (referenced by common average reference, white matter reference, or bipolar reference). For voltage data, there is one more special type "full" which loads voltage data for all electrodes.

Description

'RAVE' Context: Read and Set Context of Environments

Usage

rave_context(
  context,
  require_contexts,
  disallowed_context,
  error_msg,
  spos = 2L,
  senv,
  tpos = 1L,
  tenv
)

Arguments

Details

Context strings tells the function which context it's running, and it will affect the behaviors of functions within its environment. Because 'RAVE' modules are usually R packages, the context strings help the module writers determine where the function is running. For example, running locally, or in 'RAVE' container, or debug mode. A typical example would be get_path function. All external scripts used in R packages require to be obtained using system.file. However, because the files are subject to change, using system file function requires re-compile the package, which is time-consuming. Function get_path returns the file path relative to current working directory during the development (in "default" context), and it calls system.file when 'RAVE' instance is running.

There are four contexts: "default", "rave_module_debug", "rave_running", and "rave_running_local".

default

Default context: this means the function is running without any additional information.

rave_module_debug

Debug mode: used to develop and debug modules locally. Under the context, the function will be aware of the package that module belongs to

rave_running

If the function is running under this context, this means it's running inside of shiny application (usually within start_rave). The function will be able to get more contexts such as module ID, and current runtime environment (ExecEnvir)

rave_running_local

Similar to "rave_running", but without run-time environment. Under this context, the module is running locally without shiny. All reactive observers are disabled, and the modules will be compiled into a function with all the inputs defined by define_input as arguments, and code within "main.R" as the main body of the function.

Function rave_context uses reserved variables in the environment: .__rave_context__., .__rave_package__., .__rave_module__., and .__rave_module_instance__.. Please don't use these variables for other purposes. See ‘Examples’ for how to set and read the context.

Value

A list of current context, including the package name, module ID, and current ExecEnvir instance if running under "rave_running" context.

Examples

# ------- 1. Read/Set Context ---------

library(dipsaus)
library(rave)
# Reset context for current environment
rave_context('default')

# Read from current caller's environment
fun <- function(...){
  ctx <- rave_context()
  cat2('The function is running under context - ', ctx$context)
  cat2('The package under the context - ', ctx$package)
  cat2('Module ID is - ', ctx$module_id)
  cat2('Running instance is - ', ctx$instance)
}
fun()
## The function is running under context - default
## The package under the context - 
## ...

# Set debug context 
debug_env <- new.env()
rave_context('rave_module_debug', tenv = debug_env)
debug_env$.__rave_package__. <- 'ravebuiltins'

# With debug_env, the function is aware of the package it's under
with(debug_env, { fun() })
## The function is running under context - rave_module_debug
## The package under the context - ravebuiltins
## ...

# To set context within the function and affect the functions inide
fun2 <- function(module_id){
  # Run rave_context and then set module ID
  rave_context('rave_running_local')
  .__rave_module__. <- module_id
  fun()
}
with(debug_env, { fun2('power_explorer') })
## The function is running under context - rave_running_local
## The package under the context - ravebuiltins
## Module ID is - power_explorer
## ...

# Let's see what we can do with rave_module_debug
with(debug_env, { get_path('inst/rave.yaml') })
# When I develop the package, it returns:
## "/Users/beauchamplab/.../ravebuiltins/inst/settings.yaml"
# When I run in other places, it returns
## "/Users/beauchamplab/Library/R/3.6/library/ravebuiltins/rave.yaml"


# ------- 2. Setting behaviors for context ---------
# One way to set different behaviors is to using `ctx`
## Not run: 
fun <- function(){
  ctx <- rave_context()
  switch(ctx$context, ...)
}

## End(Not run)

# The other way is to use S3 generics provided by R syntax
fun <- rave_context_generics('fun', function(module_id, ...){})

# action for default
fun.default <- function(...){
  cat2('Function is not supposed to run under default context...',
       level = 'ERROR')
}

# for debug, set module ID and run with rave_running_local
fun.rave_module_debug <- function(module_id, ...){
  cat2('Debug mode... loading a test subject')
  # Do something ... like automatically mount_demo_subject
  # by running mount_demo_subject()
  
  rave_context('rave_running_local')
  .__rave_module__. <- module_id
  # Recall the function under rave_running_local context
  fun(module_id, ...)
}

# When running within RAVE container, local and with shiny
fun.rave_running_local <- function(...){
  ctx <- rave_context()
  cat2('Yay, running ', ctx$module_id, ' under context ',
       ctx$context, level='INFO')
}
fun.rave_running <- fun.rave_running_local

# Run in default mode, expect error message
fun('power_explorer')

# Run in debug mode
debug_env <- new.env()
rave_context('rave_module_debug', tenv = debug_env)
debug_env$.__rave_package__. <- 'ravebuiltins'

# The function will run in debug mode, then rave_running_local
with(debug_env, { fun('power_explorer') })

Description

Create S3 Generics that Respects 'RAVE' Context

Usage

rave_context_generics(
  fun_name,
  fun = function() {
 }
)

Arguments

Value

A generic function

Description

RAVE Failure Message

Usage

rave_failure(message, level = "ERROR", call = NULL, .stop = TRUE)

Arguments

Value

Error condition or stop

Description

Functions for development use

Usage

rave_ignore(...)

Arguments

Description

Import Raw Signal from Non-standard Formats

Usage

rave_import_rawdata(subject_code, project_name, launch_preprocess = TRUE)

Arguments

Description

Tools for module writers

Usage

rave_module_tools(
  env = NULL,
  data_env = getDefaultDataRepository(),
  quiet = FALSE
)

Arguments

Description

Function to change rave-options

Usage

rave_options(
  ...,
  .save = TRUE,
  launch_gui = TRUE,
  host = "127.0.0.1",
  port = NULL
)

Arguments

Description

Loads subject data along with iEEG/ECoG data into memory.

Usage

rave_prepare(
  subject,
  electrodes,
  epoch,
  time_range,
  frequency_range,
  data_types = c("power"),
  reference = "default",
  attach = "r",
  data_env = getDefaultDataRepository(),
  strict = FALSE,
  ...
)

Arguments

Description

RAVE Preprocess Function

Usage

rave_preprocess(
  sidebar_width = 3,
  launch.browser = TRUE,
  host = "127.0.0.1",
  port = NULL,
  quiet = TRUE,
  beta = FALSE,
  test.mode = FALSE,
  modules,
  ver = "3",
  theme = "purple",
  ...
)

Arguments

Description

Function to create RAVE preprocess tools

Usage

rave_preprocess_tools(env = new.env(), ...)

Arguments

Description

Get RAVE version

Usage

rave_version()

Description

Cache R Objects with Different levels

Usage

cache(
  key,
  val,
  name,
  replace = FALSE,
  global = FALSE,
  persist = FALSE,
  test = FALSE,
  temporary = FALSE,
  ...
)

## S3 method for class 'rave_running'
cache(
  key,
  val,
  name,
  replace = FALSE,
  global = FALSE,
  persist = FALSE,
  test = FALSE,
  temporary = FALSE,
  ...
)

## S3 method for class 'rave_running_local'
cache(..., global = TRUE)

## Default S3 method:
cache(..., global = TRUE)

cache_input(
  inputId,
  val = NULL,
  read_only = TRUE,
  ...,
  session = getDefaultReactiveDomain()
)

clear_cache(levels = 1)

Arguments

Value

Cached value, or val. If cache and val are both missing, then return NULL.

Examples

# global can be set to false within RAVE modules
print(cache('a', 1, name = 'data', global = TRUE)) # returns 1
print(cache('a', 2, name = 'data', global = TRUE)) # still returns 1

# clear cache (for global=TRUE)
clear_cache(levels = 1:3)
print(cache('a', 2, name = 'data', global = TRUE)) # Now returns 2

# Not run `Sys.sleep` because a is cached
print(cache('a', 2, name = 'data', global = TRUE))
print(cache('a', {Sys.sleep(10); 1}, name = 'data', global = TRUE))

# get data without key
cache(name = 'data', global = TRUE)

# clear cache that is global-only
clear_cache(levels = 2)

# Test (test=TRUE) if cache exists, if not, return value but no save
cache(name = 'abracadabra', val = 'no cache', global = TRUE, test = TRUE)
cache(name = 'abracadabra', global = TRUE)

# cache module inputs
## Not run: 
# Need to run in package module environment
cache_input('abracadabra', 'no-magic', read_only = TRUE)  

## End(Not run)

Description

Open/Close a tab in RAVE main application

Usage

close_tab(module_id, tabname)

open_tab(module_id, tabname)

Arguments

Description

Make iElvis mgrid file

Usage

read_mgrid(con, raw = FALSE)

Arguments

Author(s)

John Magnotti

Description

For debugging module packages. In all other contexts it will raise error.

Usage

reload_module_package(expose = FALSE, clear_env = FALSE)

Arguments

Description

Save data to "CSV", if file exists, rename old file

Usage

safe_write_csv(data, file, ..., quiet = FALSE)

Arguments

Description

Function to save meta data to subject

Usage

save_meta(data, meta_type, project_name, subject_code)

Arguments

Description

Function to locally save options (deprecated)

Usage

save_options()

Description

Get ‘shiny’ "input" and "output" objects under current context

Usage

getDefaultReactiveInput(session)

## Default S3 method:
getDefaultReactiveInput(session)

## S3 method for class 'rave_module_debug'
getDefaultReactiveInput(session)

## S3 method for class 'rave_running'
getDefaultReactiveInput(session = shiny::getDefaultReactiveDomain())

## S3 method for class 'rave_running_local'
getDefaultReactiveInput(session)

getDefaultReactiveOutput(session = shiny::getDefaultReactiveDomain())

## Default S3 method:
getDefaultReactiveOutput(session = shiny::getDefaultReactiveDomain())

## S3 method for class 'rave_module_debug'
getDefaultReactiveOutput(session = shiny::getDefaultReactiveDomain())

## S3 method for class 'rave_running'
getDefaultReactiveOutput(session = shiny::getDefaultReactiveDomain())

## S3 method for class 'rave_running_local'
getDefaultReactiveOutput(session = shiny::getDefaultReactiveDomain())

Arguments

Value

In shiny context, returns special reactiveValues that refers to the inputs and outputs of shiny applications. In non-shiny contexts, returns a fake environment related to current fake session, for debug purpose.

Description

Set and Return RAVE theme

Usage

set_rave_theme(
  theme,
  .set_default = FALSE,
  session = shiny::getDefaultReactiveDomain()
)

Arguments

Details

RAVE support two themes: "light" mode and "dark" mode. In "light" mode, the web application background will be light gray and white. In "dark" mode, the application background will be gray and foreground will be white.

If theme is missing and RAVE is running as web application, then it is set from current session, otherwise, the default theme is retrieved from rave_options('default_theme'). If option "default_theme" is missing, then it defaults to "light".

Value

theme under current context.

Examples

# Retrieve current theme
get_val(rave_options('default_theme'), default = 'light')

# Set light mode
set_rave_theme('light')
plot(1:10, main = 'test light mode')

# Set dark mode
set_rave_theme('dark')
plot(1:10, main = 'test dark mode')

Description

Convert module to objects used in shiny

Usage

shinirize(
  module,
  session = getDefaultReactiveDomain(),
  test.mode = TRUE,
  data_env = getDefaultDataRepository()
)

Arguments

Description

Start RAVE main application

Usage

start_rave(
  modules = NULL,
  active_module = NULL,
  launch.browser = TRUE,
  theme = "purple",
  disable_sidebar = FALSE,
  simplify_header = FALSE,
  token = NULL,
  data_repo = getDefaultDataRepository(),
  ...
)

launch_demo(
  modules = "power_explorer",
  launch.browser = TRUE,
  theme = "green",
  disable_sidebar = TRUE,
  simplify_header = FALSE,
  ...
)

start_rave2(
  host = "127.0.0.1",
  port = NULL,
  launch.browser = TRUE,
  jupyter = FALSE,
  as_job = FALSE,
  ...
)

Arguments

Description

Start 'YAEL' electrode localization

Usage

start_yael(
  host = "127.0.0.1",
  port = NULL,
  launch.browser = TRUE,
  as_job = FALSE,
  ...
)

Arguments

Description

contains subject meta information after preprocessing.

Public fields

Active bindings

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

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

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

Returns

the preprocess information correspond to the key

Method filter_all_electrodes()

filter, and returns existing electrodes

Usage

Subject$filter_all_electrodes(electrodes)

Arguments

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

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

Method clone()

The objects of this class are cloneable with this method.

Usage

Subject$clone(deep = FALSE)

Arguments

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)

Description

Create temp file in subject module folder

Usage

subject_tmpfile(
  module_id,
  fun_name = "",
  project_name,
  subject_code,
  pattern = "file_",
  data_env = getDefaultDataRepository()
)

Arguments

Description

Parse SUMA spec file

Usage

suma_spec_parse(subject, spec_file)

Arguments

Examples

## Not run: 
subject = 'Demo/YAB'
# or create subject object
subject = Subject$new('Demo', 'YAB')

# Please download sample subjects first to run
suma_spec_parse(subject)

## End(Not run)

Description

Parse AFNI BRIK/HEAD file

Usage

suma_surface_volume_parse(file_path)

Arguments

Description

Parse 'RAVE' Module and Returns Parsed Content in Environments

Usage

to_module(
  module_id,
  sidebar_width = 3,
  parse_context = c("rave_running_local", "rave_running")
)

Arguments

Description

Debug-use only, reload package, mount demo subject, and launch shiny app

Usage

view_layout(
  module_id,
  sidebar_width = 3,
  launch.browser = TRUE,
  reload = TRUE,
  ...
)

Arguments

Description

The code was translated from Matlab script written by Brett Foster, Stanford Memory Lab, 2015 with permission to use in 'RAVE'.

Usage

wavelet(data, freqs, srate, wave_num, demean = TRUE)

Arguments

Details

Decompose time series data into time-frequency representation (spectral decomposition) using wavelet transform. Employs "Morlet" wavelet method (gaussian taper sine wave) to obtain the analytic signal for specified frequencies (via convolution).

Description

Returns wavelets to be used for wavelet function

Usage

wavelet_kernels(freqs, srate, wave_num)

Arguments