wfdb_io: I/O of WFDB-compatible signal & header files from EP...
In EGM: Evaluating Cardiac Electrophysiology Signals

wfdb_io

R Documentation

I/O of WFDB-compatible signal & header files from EP recording systems

Description

This function allows for WFDB files to be read from any WFDB-compatible system, and also allows writing out WFDB-compatible files from specific EP recording systems, as indicated in the details section. Writing WFDB leads to creation of both a dat (signal) and hea (header) file. These are both required for reading in files as well.

Usage

write_wfdb(
  data,
  record,
  record_dir,
  wfdb_path = getOption("wfdb_path"),
  header = list(frequency = 250, gain = 200L, label = character()),
  info_strings = list(),
  ...
)

read_wfdb(
  record,
  record_dir = ".",
  annotator = NA_character_,
  wfdb_path = getOption("wfdb_path"),
  begin = 0,
  end = NA_integer_,
  interval = NA_integer_,
  units = "digital",
  channels = character(),
  ...
)

read_signal(
  record,
  record_dir = ".",
  wfdb_path = getOption("wfdb_path"),
  begin = 0L,
  end = NA_integer_,
  interval = NA_integer_,
  units = "digital",
  channels = character(),
  ...
)

read_header(record, record_dir = ".", wfdb_path = getOption("wfdb_path"), ...)

Arguments

`data`	Can either be an `egm` object, or a `data.frame` (or similar) object. The function will appropriately set defaults based on the type. `egm` = Will extract signal and header data directly from object, and thus is simplest to convert to a WFDB format `signal_table` = This is a customized `data.table` class that has an invariant column containing sample information. `data.frame` or `data.table` = Must have a column that represents a time point or index, and columns that represent signal values (preferably integers)
`record`	String that will be used to name the WFDB record. Cannot include extensions, and is not a filepath. alphanumeric characters are acceptable, as well as hyphens (-) and underscores (_)
`record_dir`	File path of directory that should be used read and write files. Defaults to current directory.
`wfdb_path`	Path that leads to installed `wfdb` software package on device. Needs to be directly set using `set_wfdb_path()`. Obtained from the system options on loading of the package, `getOption('wfdb_path')`
`header`	A header file is an optional named list of parameters that will be used to organize and describe the signal input from the data argument. If the type is given, specific additional elements will be searched for, such as the low or high pass filters, colors, or other signal attributes. At minimum, the following elements are required (as cannot be calculated): frequency = sample frequency in Hertz as `integer` label = vector of names for each channel as `character` start_time = date/time object
`info_strings`	A `list` of strings that will be written as an appendix to the header file, usually containing information about the channels, (e.g. list of colors, extra labels, etc).
`...`	Additional arguments to be passed to the function
`annotator`	String that is the name of a WFDB-compatible annotation type, serving as the extension for the file that is written containing that annotation. Please see `read_annotation()` and `write_annotation()` for further details.
`begin`, `end`, `interval`	Timepoint as an `integer` (representing seconds), which is converted to an index position based on sampling frequency. The default is to start at the beginning of the record. If `end` or `interval` are given, the earlier of the two will be returned. The `end` argument gives a time index to read until. The `interval` argument is the length of time past the start point.
`units`	A `character` string representing either digital (DEFAULT) or physical units that should be used, if available. digital = Index in sample number, signal in integers (A/D units) physical = Index in elapsed time, signal in decimal voltage (e.g. mV). This will include 1 additional row over the header/column names that describes units
`channels`	Either the signal/channel in a `character` vector as a name or number. Allows for duplication of signal or to re-order signal if needed. If nothing is given, will default to all channels available.

Value

Depends on if it is a reading or writing function. For writing, will output an WFDB-based object reflecting the function. For reading, will output an extension of a data.table object reflecting the underlying function (e.g. signal_table() will return an object of class).

Functions

write_wfdb(): Writes out signal and header data into a WFDB-compatible format from R.
read_wfdb(): Reads a multicomponent WFDB-formatted set of files directly into an egm object. This serves to pull together read_signal(), read_header(), and read_annotation() for simplicity.
read_signal(): Specifically reads the signal data from the WFDB binary format, returning a signal_table object for evaluation in the R environment
read_header(): Specifically reads the header data from the WFDB header text format, returning a header_table object for evaluation in the R environment