In this vignette, a brief description of the RHRV package is presented. Due to the large collection of features that RHRV offers, we shall only refer to the most important functionality to perform a basic Heart Rate Variability (HRV) analysis. The interested reader is referred to the free tutorial for further information.
This vignette assumes that the user has some basic knowledge of the R environment. If this is not your case, you can find a nice introduction to R in the R project homepage. The R project homepage also provides an R Installation and Administration guide. Once you have download and installed R, you can install RHRV by typing:
You can also install it by downloading it from the CRAN. Once the
download has finished, open R, move to the directory
where you have download it (by using the R command
setwd
and type:
Here, XXX is the version number of the library. To start using the library, you should load it by using:
We propose the following basic program flow to perform a basic HRV analysis using the RHRV package:
We shall deal with each of these points in the following sections. All the examples of this vignette will use the example beats file “example.beats” that may be downloaded from here. Additionally, the data from this file has been included in RHRV. The user can access this data executing:
# HRVData structure containing the heart beats
data("HRVData")
# HRVData structure storing the results of processing the
# heart beats: the beats have been filtered, interpolated, ...
data("HRVProcessedData")
The example file is an ASCII file that contains the beats positions obtained from a 2 hours electrocardiogram (ECG), with one beat position per row. The subject of the ECG is a patient suffering from paraplegia and hypertension (systolic blood pressure above 200 mm-Hg). During the recording, he is supplied with prostaglandin E1 (a vasodilator that is rarely employed) and systolic blood pressure fell to 100 mm-Hg for over an hour. Then, the blood pressure increased slowly up to approximately 150 mm-Hg.
RHRV uses a custom data structure called
HRVData
to store all HRV information related to the signal
being analysed. The following Figure summarizes the most important
fields in the HRVData
structure. HRVData
is
implemented as a list object in R language. This list
contains all the information corresponding to the signal to be analysed,
some parameters generated by the pre-processing functions and the HRV
analysis results. It must be noted that, since the HRVData
structure is a list, each of its fields can be accessed using the
$
operator of the R language.
After creating the empty HRVData
structure the next step
should be loading the signal that we want to analyse into this
structure. RHRV imports data files containing heart
beats positions. Supported formats include ASCII
(LoadBeatAscii
function), EDF
(LoadBeatEDFPlus
), Polar (LoadBeatPolar
),
Suunto (LoadBeatSuunto
) and WFDB data files
(LoadBeatWFDB
). For the sake of simplicity, we will focus
in ASCII files containing one heart beat occurrence time per line. We
also assume that the beat occurrence time is specified in seconds. For
example, let’s try to load the “example.beats” file, whose first lines
are shown below. Each line denotes the occurrence time of each
heartbeat.
0
0.3280001
0.7159996
1.124
1.5
1.88
...
In order to load this file, we may write:
## Loading beats positions for record: example.beats
## Path: beatsFolder
## Scale: 1
## Date: 01 / 01 / 1900
## Time: 00 : 00 : 00
## Number of beats: 17360
The console information is only displayed if the verbose mode is on.
The Scale
parameter is related to the time units of the
file. 1 denotes seconds, 0.1 tenth of seconds and so on. The
Date
and Time
parameters specify when the file
was recorded. The RecordPath
can be omitted if the
RecordName
is in the working directory.
Further information about this function and other input formats may be found in the online tutorial.
To compute the HRV time series the BuildNIHR
function
can be used (Build Non Interpolated Heart Rate). This function
constructs both the RR and instantaneous heart rate (HR) series. We will
refer to the instantaneous Heart Rate as the niHR (non interpolated
Heart Rate) series. Both series are stored in the HRVData
structure.
## Calculating non-interpolated heart rate
## Number of beats: 17360
A Filtering operation must be carried out in order to eliminate
outliers or spurious points present in the niHR time series with
unacceptable physiological values. Outliers present in the series
originate both from detecting an artefact as a heartbeat (RR interval
too short) or not detecting a heartbeat (RR interval too large). The
outliers removal may be both manual or automatic. In this quick
introduction, we will use the automatic removal. The automatic removal
of spurious points can be performed by the FilterNIHR
function. The FilterNIHR
function also eliminates points
with unacceptable physiological values.
## Filtering non-interpolated Heart Rate
## Number of original beats: 17360
## Number of accepted beats: 17248
In order to be able to perform spectral analysis in the frequency
domain, a uniformly sampled HR series is required. It may be constructed
from the niHR series by using the InterpolateNIHR
function,
which uses linear (default) or spline interpolation. The frequency of
interpolation may be specified. 4 Hz (the default value) is enough for
most applications.
# Note that it is not necessary to specify freqhr since it matches with
# the default value: 4 Hz
hrv.data = InterpolateNIHR(hrv.data, freqhr = 4)
## Interpolating instantaneous heart rate
## Frequency: 4 Hz
## Number of beats: 17248
## Number of points: 29592
Before applying the different analysis techniques that RHRV provides,
it is usually interesting to plot the time series with which we are
working. The PlotNIHR
function permits the graphical
representation of the niHR series whereas the PlotHR
function permits to graphically represent the interpolated HR time
series. The two plots are usually very similar. For example, we could
type:
## Plotting non-interpolated instantaneous heart rate
## Number of points: 17248
As seen in the previous figure, the patient initially had a heart rate of approximately 160 beats per minute. Approximately half an hour into record the prostaglandina E1 was provided, resulting in a drop in heart rate to about 130 beats per minute during about 40 minutes, followed by a slight increase in heart rate.
The simplest way of performing a HRV analysis in
RHRV is using the time analysis techniques provided by
the CreateTimeAnalysis
function. This function computes the
most widely used time-domain parameters and stores them in the
HRVData
structure. The most interesting parameter that the
user may specify is the width of the window that will be used to analyse
short segments from the RR time series (size
parameter, in
seconds). Concretely, several statistics will be computed for each
window. By studying how these statistics evolve through the recording, a
set of time parameters will be computed (For example, the
SDANN
and SDNNIDX
parameters). Other important
argument that can be tuned is the interval width of the bins that will
be used to compute the histogram (interval
parameter). As
an alternative to the interval
parameter, the user may use
the numofbins
parameter to specify the number of bins in
the histogram. A typical value for the size
parameter is
300 seconds (which is also the default value), whereas that a typical
value for the interval
is about 7.8 milliseconds (also
default value).
If the verbose mode is on, the program will display the results of
the calculations on the screen. Otherwise, the user must access the
“raw” data using the $
operator of the R
language.
Finally, we show a complete example for performing a basic time-domain analysis. The console output is also shown. It should be noted that it is not necessary to perform the interpolation process before applying the time-domain techniques since these parameters are calculated directly from the non interpolated RR-time series.
hrv.data = CreateHRVData()
hrv.data = SetVerbose(hrv.data,FALSE)
hrv.data = LoadBeatAscii(hrv.data,"example.beats","beatsFolder")
hrv.data = BuildNIHR(hrv.data)
hrv.data = FilterNIHR(hrv.data)
hrv.data = SetVerbose(hrv.data,TRUE)
hrv.data = CreateTimeAnalysis(hrv.data,size=300,interval = 7.8125)
## Creating time analysis
## Size of window: 300 seconds
## Width of bins in histogram: 7.8125 milliseconds
## Number of windows: 24
## Data has now 1 time analyses
## SDNN: 39.7449 msec.
## SDANN: 31.1059 msec.
## SDNNIDX: 24.9566 msec.
## pNN50: 9.306 %
## SDSD: 30.8642 msec.
## r-MSSD: 30.8633 msec.
## IRRR: 56 msec.
## MADRR: 16 msec.
## TINN: 172.0945 msec.
## HRV index: 11.014
# We can access "raw" data... let's print separately, the SDNN
# parameter
cat("The SDNN has a value of ",hrv.data$TimeAnalysis[[1]]$SDNN," msec.\n")
## The SDNN has a value of 39.74489 msec.
A major part of the functionality of the RHRV
package is dedicated to the spectral analysis of HR signals. Before
performing the frequency analysis, a data analysis structure must be
created. Such structure shall store the information extracted from a
variability analysis of the HR signal as a member of the
FreqAnalysis
list, under the HRVData
structure. Each analysis structure created is identified by a unique
number (in order of creation). To create such an analysis structure, the
CreateFreqAnalysis
function is used.
## Creating frequency analysis
## Data has now 1 frequency analysis
Notice that, if verbose mode is on, the
CreateFreqAnalysis
function informs us about the number of
frequency analysis structures that have been created. In order to select
a particular spectral analysis, we will use the
indexFreqAnalysis
parameter in the frequency analysis
functions.
The most important function to perform spectral HRV analysis is the
CalculatePowerBand
function. The
CalculatePowerBand
function computes the spectrogram of the
HR series in the ULF (Ultra Low Frequency), VLF (Very
Low Frequency), LF (Low Frequency) and HF (High
Frequency) bands using the Short Time Fourier Transform (STFT) or
wavelets. Boundaries of the bands may be chosen by the user. If
boundaries are not specified, default values are used: ULF, [0,
0.03] Hz; VLF, [0.03, 0.05] Hz; LF, [0.05, 0.15] Hz;
HF, [0.15, 0.4] Hz. The type of analysis can be selected by the
user by specifying the type
parameter of the
CalculatePowerBand
function. The possible options are
either "fourier"
or "wavelet"
. Because of the
backwards compatibility, the default value for this parameter is
"fourier"
.
When using the STFT to compute the spectrogram using the
CalculatePowerBand
function, the user may specify the
following parameters related with the STFT:
Size
: the size of window for calculating the
spectrogram measured in seconds. The RHRV package
employs a Hamming window to perform the STFT.Shift
: the displacement of window for calculating the
spectrogram measured in seconds.Sizesp
: the number of points for calculating each
window of the STFT. If the user does not specify it, the program selects
a proper length for the calculations (it selects sizesp
so
that sizesp
= 2m, for some m ∈ ℕ).When using CalculatePowerBand
, the
indexFreqAnalysis
parameter (in order to indicate which
spectral analysis we are working with) and the boundaries of the
frequency bands may also be specified.
As an example, let’s perform a frequency analysis in the typical HRV spectral bands based on the STFT . We may select 300 s (5 minutes) and 30 s as window size and displacement values because these are typical values when performing HRV spectral analysis. We let the program choose the value of the zero-padding. Thus, we may write:
hrv.data = CreateHRVData( )
hrv.data = SetVerbose(hrv.data,FALSE)
hrv.data = LoadBeatAscii(hrv.data,"example.beats","beatsFolder")
hrv.data = BuildNIHR(hrv.data)
hrv.data = FilterNIHR(hrv.data)
hrv.data = InterpolateNIHR (hrv.data, freqhr = 4)
hrv.data = CreateFreqAnalysis(hrv.data)
hrv.data = SetVerbose(hrv.data,TRUE)
# Note that it is not necessary to write the boundaries
# for the frequency bands, since they match
# the default values
hrv.data =
CalculatePowerBand(hrv.data , indexFreqAnalysis = 1,
size = 300, shift = 30, type = "fourier",
ULFmin = 0, ULFmax = 0.03, VLFmin = 0.03, VLFmax = 0.05,
LFmin = 0.05, LFmax = 0.15, HFmin = 0.15, HFmax = 0.4 )
## Calculating power per band
## Using Fourier analysis
## Windowing signal... 237 windows
## Power per band calculated
Alternatively, since most values of the arguments match its default values we could have written:
When using Wavelet analysis with the CalculatePowerBand
function, the user may specify:
wavelet
: mother wavelet used to calculate the
spectrogram. Some of the most widely used Wavelets are available: Haar
("haar"
), extremal phase ("d4"
,
"d6"
, "d8"
and "d16"
) and the
least asymmetric Daubechies ("la8"
, "la16"
and
"la20"
) and the best localized Daubechies
("bl14"
and "bl20"
) Wavelets among others. The
default value is "d4"
. The name of the wavelet specifies
the family
(the family determines the shape of the Wavelet
and its properties) and the length of the wavelet. For example,
"la8"
belongs to the Least Asymmetric family and has a
length of 8 samples. We may give a simple advice for wavelet selection
based on the wavelet’s length: shorter wavelets usually have better
temporal resolution, but worse frequency resolution. On the other hand,
longer wavelets usually have worse temporal resolution, but they provide
better frequency resolution. Better temporal resolution means that we
can study shorter time intervals. On the other hand, a better frequency
resolution means better frequency discrimination. That is,
shorter wavelets will tend to fail when discriminating close
frequencies.
bandtolerance
: maximum error allowed when the
Wavelet-based analysis is performed. It can be specified as an absolute
or a relative error depending on the relative
parameter
value. Default value is 0.01.
relative
: logic value specifying which type of band
tolerance shall be used: relative (in percentage) or absolute (default
value). For the sake of simplicity, in this document we will use the
absolute band tolerance.
Let’s analyse the same frequency bands as before but using the
wavelet-algorithm. For the sake of simplicity, we will use an absolute
tolerance of 0.01 Hz. We may select the least asymmetric Daubechies of
width 8 ("la8"
) as wavelet, since it provides a good
compromise between frequency and time resolution. Thus, we may
write:
hrv.data = CreateHRVData( )
hrv.data = SetVerbose(hrv.data,FALSE)
hrv.data = LoadBeatAscii(hrv.data,"example.beats","beatsFolder")
hrv.data = BuildNIHR(hrv.data)
hrv.data = FilterNIHR(hrv.data)
hrv.data = InterpolateNIHR (hrv.data, freqhr = 4)
hrv.data = CreateFreqAnalysis(hrv.data)
hrv.data = SetVerbose(hrv.data,TRUE)
# Note that it is not necessary to write the boundaries
# for the frequency bands, since they match the default values
hrv.data =
CalculatePowerBand( hrv.data , indexFreqAnalysis = 1,
type = "wavelet", wavelet = "la8",
bandtolerance = 0.01, relative = FALSE,
ULFmin = 0, ULFmax = 0.03, VLFmin = 0.03, VLFmax = 0.05,
LFmin = 0.05, LFmax = 0.15, HFmin = 0.15, HFmax = 0.4 )
## Calculating power per band
## Using Wavelet analysis
## Power per band calculated
In the previous examples we have used just one frequency analysis to
illustrate the basic use of CalculatePowerBand
. However, it
is possible to create and use the same HRVData
for
performing several spectral analysis. When we do this, we use the
parameter indexFreqAnalysis
to indicate which spectral
analysis we are working with. For example, we could perform both Fourier
and wavelet based analysis:
# ...
# create structure, load beats, filter and interpolate
hrv.data = CreateFreqAnalysis(hrv.data)
hrv.data = SetVerbose(hrv.data, FALSE)
# use freqAnalysis number 1 for perfoming
# Fourier analysis. This time, we do not
# write the band's boundaries
hrv.data = CalculatePowerBand(hrv.data , indexFreqAnalysis = 1,
size = 300, shift = 30, sizesp = 2048,
type = "fourier")
# use freqAnalysis number 2 for perfoming
# wavelet analysis. Note the indexFreqAnalysis = 2!!!
hrv.data = CreateFreqAnalysis(hrv.data)
hrv.data = CalculatePowerBand(hrv.data, indexFreqAnalysis= 2,
type = "wavelet", wavelet = "la8",
bandtolerance = 0.01, relative = FALSE)
RHRV also includes plotting utilities for
representing the spectrogram of each frequency band: the
PlotPowerBand
function. PlotPowerBand
receives
as inputs the HRVData
structure and the index of the
frequency analysis that the user wants to plot
(indexFreqAnalysis
argument). Optionally, the user can
specify additional parameters for modifying the plots (whether to use or
not normalized plots, specify the y-axis, etc.). For the sake of
simplicity we will only use the ymax
parameter (for
specifying the maximum y-axis of the power bands plot) and the
ymaxratio
parameter (for specifying the maximum y-axis in
the LF/HF plot).
If we want to plot the power bands computed in the previous example, we may use:
The previous Figures illustrate some of the most important differences between Fourier and wavelet-based analysis. The most important differences may be summarized as follows: