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An open source tool for heart rate variability spectral analysis.

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journal homepage: www.intl.elsevierhealth.com/journals/cmpb

An open source tool for heart rate variability spectral

analysis

L. Rodríguez-Liñares ∗ , A.J. Méndez, M.J. Lado, D.N. Olivieri, X.A. Vila, I. Gómez-Conde
Dpto. Informática University Vigo, Spain1

a r t i c l e i n f o a b s t r a c t

Article history: In this paper we describe a software package for developing heart rate variability analysis.
Received 15 October 2009 This package, called RHRV, is a third party extension for the open source statistical envi-
Received in revised form ronment R, and can be freely downloaded from the R-CRAN repository. We review the state
26 April 2010 of the art of software related to the analysis of heart rate variability (HRV). Based upon this
Accepted 24 May 2010 review, we motivate the development of an open source software platform which can be used
for developing new algorithms for studying HRV or for performing clinical experiments. In
Keywords: particular, we show how the RHRV package greatly simplifies and accelerates the work of
Heart rate variability the computer scientist or medical specialist in the HRV field. We illustrate the utility of our
Open source package with practical examples.
Apnea © 2010 Elsevier Ireland Ltd. All rights reserved.
Signal processing

three relevant peaks: the VLF (very-low frequency) contai-

1. Introduction ning frequencies below 0.03 Hz, the LF (low frequency),
having frequencies between 0.03 and 0.15 Hz, and the HF
In ancient times, physicians believed that our heart beats regu-
(high frequency) peaks which lie between 0.18 and 0.4 Hz.
larly with a fixed rate, rising or falling due to external stimulus,
Using drugs for selectively blocking different components
such as fear, anxiety, relaxations, etc. When it was possible to
of the neurovegetative control systems, Akselrod discovered
measure the heart rhythm with more precision, it was disco-
that the parasympathetic system modulates the LF and HF
vered that it was not constant but experienced some amount
peaks, the sympathetic system alters the LF peak, and the
of variability. Until the past century, physicians thought this
renin–angiotensin system modulates the VLF peak. A prac-
variability was simply noise and had no clinical relevance.
tical consequence of this experiment was that the heart rate
It wasn’t until the period between 1970 and 1990, that key
variability could be used as an indicator or indirect measure of
research findings demonstrated that this variability had phy-
the status of the neurovegetative control system.
siological origins and was related to phenomena such as the
HRV has been an active research field since the 1990s. Seve-
respiratory rate or the neurovegetative control system [1,2].
ral analysis techniques have been developed and improved
Explicit relationships between spectral components of
[4,5] including time indices, spectral analysis, and non-linear
heart rate variability (HRV) and the different components
analysis. The relation of HRV with some pathologies such
of the neurovegetative control systems were experimen-
as myocardial infarction, sudden cardiac death, heart failure,
tally demonstrated by Akselrod et al. [3], who described
hypertension, and ischaemia has been established in several

∗
Corresponding author at: Escuela Superior de Ingeniera Informática, As Lagoas, s/n, 32004 Ourense, Spain. Tel.: +34 988387009.
+34 986813929.
E-mail addresses: leandro@uvigo.es (L. Rodríguez-Liñares), mrarthur@uvigo.es (A.J. Méndez), mrpepa@uvigo.es
(M.J. Lado), olivieri@uvigo.es (D.N. Olivieri), anton@uvigo.es (X.A. Vila), igconde@correo.ei.uvigo.es (I. Gómez-Conde).
1
http://www.milegroup.net.
0169-2607/$ – see front matter © 2010 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.cmpb.2010.05.012
40 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
studies [6,7]. As an indication that HRV continues to be an
active practical field with unresolved problems, there were 21
papers directly related with HRV in the recent 2009 Computers
in Cardiology Conference [8].
Unfortunately, clinical practitioners have not included HRV
analysis in their standard diagnostic protocols. As a conse-
quence, medical device manufacturers have not traditionally
placed a high priority on including this type of analysis in their
products [7]. First generation monitoring systems of the 1990s
permitted the analysis of only a limited number of basic para-
meters in the time domain and provided only rudimentary
spectral analysis. The principal disadvantage of these early
systems, however, was the inherent limitations for modifying
measurement parameters as well as the inflexibility of data
format interchange.
Modern commercial monitoring systems have impro-
ved considerably due to greater computational capability of
embedded systems and to the ability to include a greater range
of flexibility. For example, our research related to signal pro-
cessing of apnea, a chronic sleep disorder, has benefitted from
recent commercial polysomnographic systems such as the
Ultrasom Network by Nicolet and the Somnoscreen of Sonome-
dics, where variability analysis may be performed both in the
time and frequency domain. Such systems also offer the pos-
sibility of using different standard formats required by various
data processing software and hardware tools.
Despite these improvements, present commercial systems
are designed for clinical uses and do not have the program-
mability needed by researchers in signal processing, looking
for new and yet unforeseen discriminators or algorithms. For
this task, researchers rely upon software post-processing. As
an example, such systems do not directly permit the custo-
mization of the spectral bands, nor other analysis parameters
such as the size of temporal windows, type of spectral esti-
mators, etc. Thus, researchers rely upon software tools, and
not commercial clinical systems for exploring new diagnostic
techniques.
In this paper we present a software tool useful for resear-
chers in the HRV field. The paper is structured as follows. In
Section 2 we review the state of the art in the field of software
for HRV analysis. Section 3 contains a general description of
our software package and an example for presenting the use
of our tool. In Section 4, we present another example in order
to explain how our tool could be used to validate a medical
hypothesis related with HRV. Finally a discussion section is
included in which we summarize the main advantages of our
software tool and describe future work.
2. Background
The development of our HRV software package grew out of
what we perceived as a need to unify software functionality
into one open source and easily extendible tool. We based
our decision to develop the package in the R-language after
a thorough bibliographic review, paying careful attention to
the software tools being employed and developed.
The majority of researchers have obtained their data from
commercial acquisition systems or from a standard database
such as Physionet [9]. Besides, a large collection of ava-
laible tools to study HRV, consists mostly of custom software
packages or a loose collection of utilities (a significant number
of them using Matlab or Octave). Some authors describe their
algorithms, yet do not give specifics of the implementation
platform or language. Among the few authors that describe
specific environments for studying HRV signals, many of the
tools are proprietary and not made available in the public
domain for use by other researchers.
Recently, National Instruments described how variability
analysis can be performed in LabVIEW [10]. While they freely
offer both the LabVIEW model and documentation, the Lab-
VIEW software platform is a commercial product and is more
frequently used by hardware designers or experimentalists
than by computer scientists working in the field of medical
informatics.
We have previously mentioned Physionet, which is a web
portal containing an extensive database of physiologic signals
as well as software tools, such as the WFDB [11] library, that
are freely available. Amongst the utilities offered at this site is
the C language based HRV Toolkit [12] that utilizes the WFDB
library to obtain signals of heart rate and parameters of varia-
bility, both in the time and frequency domain. This is a basic
software tool and requires installation of both the libraries and
the HRV Toolkit on systems that support C.
Recently, Physionet published a news item on their web-
site [13] which suggests three different options available for
performing HRV analysis with their databases:
• The preliminary version of our package RHRV [14].
• A collection of Matlab scripts [15] which implement func-
tions for the linear and non-linear spectrum. Nonetheless,
these Matlab scripts do not include convenient interfaces
for importing data, nor does it include specific graphics uti-
lities.
• A software package called KUBIOS-HRV [16,17]. The latest
version of this software is based on Matlab and is multi-
platform. It imports ASCII files as well as data files from
Polar and Suunto heart rate monitors (HRM and SDF/STE
files, respectively). It has a well designed graphical interface
and performs analysis in time and frequency domain as well
as non-linear dynamical studies.
The most complete and useful software tool that we
encountered for HRV analysis is the aHRV, developed by Nevro-
kard [18]. This is a very well designed commercial tool that
provides many options. With this software, heart rate data
from multiple sources such as ASCII files, binary files in Euro-
pean Data Format [19], or other proprietary formats may be
imported. Other aspects of this software include time and
frequency analysis, flexibility for modifying input processing
parameters, and a well designed user interface. Nevorkard also
offers other modified versions of this tool, such as LT-HRV for
analyzing segmented ECG records or OSAS for apnea scree-
ning.
As researchers, however, we believe that our use of the
aHRV system has several drawbacks. Foremost, it is a closed
commercial tool, which is not typically an issue for hospital
users, but poses significant limitations for researchers interes-
ted in developing new algorithms. Thus, beyond the provided
functionalities, it isn’t possible to implement new algorithms,
 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Fig. 1 – Extracting useful information from the spectral
content of the heart-rate signal.
define new plots, or configure new statistical tests. Thus,
this software package is a good solution for physicians with
concrete clinical studies in mind, however it is not suitable for
researches with mathematical and programming skills who
would like to experiment with new methodologies, integrate
with other software tools, adapt the interfaces to different
types of users, etc.
3. Software description
In this section we describe our RHRV software package. First,
we briefly review the characteristics of the R-statistical envi-
ronment which are fundamental to our package. Next, we
provide an overview of the functions in our RHRV package and
a complete example.
3.1. The R environment/language
The R language [20,21] is an open source software idiom for
statistical computing and graphics that is presently used by a
growing number of researchers. The R language is an imple-
mentation of the S language, which was inspired by dialects
of Lisp. R is distributed under the GNU project and can be run
on a wide variety of UNIX, Windows and MacOSX platforms.
The main characteristics of the R language are:
• Its core functionality is for statistical calculations.
• It is highly extensible via third party packages, many of
which are supplied with the R distribution and others are
available through the CRAN family of Internet sites and
cover a very wide range of applications.
• It consists of a rich programming language with user defi-
ned data types, a suite of mathematical operators for
vectors and matrices, and an integrated collection of data
analysis tools.
• It contains facilities for highly customized plots.
3.2. The RHRV package
The general processing steps involved in extracting useful
information from the spectral content of the heart-rate signal
is shown in Fig. 1. These steps define the basic design and
process pipeline of our software package, RHRV.
41
Fig. 2 – The central data structure used in RHRV.
RHRV uses a custom data structure to store all information
related to digital recordings from a polysomnograph. While a
more detailed description of the data structure may be consul-
ted elsewhere [22], its most salient aspects shall be described
here.
The package uses a data structure called HRVData which is
described graphically in Fig. 2 and is implemented as a list
data object in the R language. This list contains fields corres-
ponding to imported data as well as parameters generated
by our pre-processing functions to perform heart rate varia-
bility analysis. It is also possible to perform various analyses
with different parameters and the results are stored in their
respective structure which can be very useful for comparing
purposes.
Three types of data substructures are defined, corres-
ponding to time-domain, frequency-domain and non-linear
analysis. The present version of our package only imple-
ments frequency analysis functions, so the other structures
are implemented as placeholders for future development.
The HRVData structure has the following fields:
• Beat: a dataframe which stores the instantaneous heart rate
data. It contains the position of beats (Time) and the non-
interpolated or instantaneous frequency (niHR).
• Episodes: a dataframe containing fields to store the begin-
ning, type, duration and a numerical value associated with
each episode (InitTime, Type, Duration and Value, res-
pectively).
• HR: a vector containing the instantaneous interpolated heart
rate data.
• FreqAnalysis: list of objects of FreqAnalysis type contai-
ning results of one or more frequency analysis.
• Other fields containing the heart rate interpolation fre-
quency (Freq HR), a string used as file extension by
loading/writing functions (Ext) and the date and time asso-
ciate with the record (datetime).
The package RHRV provides utility functions for importing
heart rate time series data, analyzing their variability, and
plotting and/or exporting the analysis results. These functions
are summarized graphically in Fig. 3 and can be called from
custom user code, allowing transparent interoperability with
other R-packages.
RHRV imports data files containing heart beat posi-
tions both in WFDB and ASCII fomat (LoadBeatWFDB() and
LoadBeatAscii(), respectively). LoadBeatWFDB() acts as a
wrapper for the C-language utility program rdann, provided by
Physionet, which imports data from a record in WFDB format.
42 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Fig. 3 – Main functions in the RHRV package.
The instantaneous heart rate can be defined as the inverse
of the time separation between two consecutive heart beats.
The core utility BuildNIHR() implements this operation and
fills the niHR field of the Beat dataframe.
Intervals within the heart beat time series, which are of
physiologic interests, are annotated in so-called episode files.
The RHRV package provides functions for loading ASCII or
WFDB formatted files (LoadEpisodesAscii() and LoadAp-
neaWFDB()). Besides, manual episodes generation is possible
with AddEpisodes(). Another option is to generate new
episodes from existing ones: this is done with GenerateE-
pisodes(), which inserts an annotation with a specific time
duration before or after an existing episode event.
Outlier or spurious points may be deleted manually or auto-
matically. In order to delete outliers manually, a graphical
editor is provided (from the function call EditNIHR()) so that
the user may interactively delete ranges of points from the
instantaneous heart rate analysis. The elimination of these
points does not affect the calculation of beat intervals or
the subsequent interpolation since the input data from the
ECG consists of a sequence of absolute time positions. Since
episodes are identified by their beginning instants and their
durations and both magnitudes are absolute times, removal
of artifacts has no effect on them. Automatic removal of out-
liers can also be performed by the FilterNIHR() function.
This function is based on an algorithm developed by one of
the authors [4], that uses adaptive thresholding for rejecting
beats whose value exceeds the cumulative mean threshold.
The filter also eliminates points that are not within acceptable
physiological values.
An evenly spaced heart rate series may be obtained with
InterpolateNIHR(), which uses cubic spline interpolation.
This functions fills the HR field of HRVData structure.
Functions are provided to graphically represent the non-
interpolated and interpolated heart rate (PlotNIHR() and
PlotHR(), respectively). These functions allow the user to
include episodic information in the plots.
A large part of the core functionality of the RHRV
package is dedicated to the spectral analysis of heart rate
signals. As can be observed in Fig. 2, several analyses
(with different input parameters) may be performed and
stored in parallel. The package includes functions for cal-
culating the spectrogram and the energy contained within
specified spectral bands (CalculateSpectrogram() and Cal-
culatePowerBand()). The function CalculatePowerBand()
calculates the spectrogram and then obtains the power in four
spectral bands: ULF, VLF, LF and HF. Default limits for these
bands and the size and shift of the analysis window are spe-
cified but can be modified by the user.
RHRV includes specialized plotting utilities for represen-
ting the spectrogram and the power in each spectral band
(PlotSpectrogram() and PlotPowerBand(), respectively).
Episodic information can be included in the plots.
The package provides functions to split heart rate signals
and power band arrays into new data structures corresponding
to intervals inside and outside episodes (SplitHRbyEpi-
sodes() and SplitPowerBandByEpisodes()). The former is
used by AnalyzeHRbyEpisodes() to perform a comparison of
HR data inside and outside episode events.
 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Listing 1 – A complete example of RHRV in use.
For a more detailed description of each of these functions,
the software package is distributed with an extensive user
manual that conforms to the standards of R-package distri-
butions of the CRAN repository.
3.3. A practical example
In this section, an illustrative example of a heart rate variabi-
lity analysis with our software package is presented. Listing 1
shows an example program for studying apnea signal data. In
particular, this example illustrate how data is loaded and pro-
cessed, how plots are generated (including physiologic episode
43
information), and how this information is used for parameter
comparison.
The example uses a data record (a03) from the Apnea-
ECG database [23], constructed for the 2000 Computers in
Cardiology Challenge, which can be downloaded from the Phy-
siobank collection [24].
An analysis of Listing 1 is useful to describe the program
logic and flow, as well as the different parts of the package that
are involved:
• All the functions in the package accept a logical
argument verbose that instructs the program to
44 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50

Fig. 4 – Plot obtained with function PlotNIHR().

Fig. 5 – Removing artifacts with EditNIHR().

show information of the performed actions in the R

console.
• Data structures must be initialized before using them. Line 6 performs the following actions: (a) it splits the sequence
creates the variable md for storing all the data of this record of interpolated heart rate values into two vectors contai-
and is used by all other functions as a global parameter. Line ning samples inside and outside the episode specified in
28 creates a new frequency analysis which can be referred the argument tag, and (b) it applies a function to each of
to by an index (lines 29 to 33). This structure allows md to these vectors returning a list with two results InEpisodes
store different frequency analysis, as can be seen in Fig. 2. and OutEpisodes. The output of lines 24 to 26 can be seen in
• Each episode is labelled with a tag. Subsequently, vectors Listing 2. In this example, a very simple user-defined func-
of tags can be used by functions involving episodes. For tion (CalPower()) was used, but any other function could
example, in line 15 only episodes with the specified tags be used independent of its complexity, so that training or
are included in the plot, while in line 22 all the episodes are testing procedures could easily be implemented.
represented.
• The example shows how RHRV manipulates episodic infor-
mation:
Line 10 loads episodes from an external file.
Line 11 adds a new episode labelled “MANUAL” in order to
define an interval with a length of 1000 seconds with start
value beginning at second 4300. More than one episode
can be added simultaneously using vectors as arguments.
Lines 12 and 13 create episodes with duration 480 seconds
120 seconds before (“PREV APN”) and after (“POST APN”)
each episode “APN”.
• Plots are generated in lines 15, 22 and 30 (Figs. 4, 6 and 7). As
stated, episodic information can be specified using the argu-
ment tag. While line 15 (Fig. 4) plots the non-interpolated
heart rate, line 22 (Fig. 6) plots the heart rate after outlier
removal (lines 17 and 18) and interpolation (line 20).
• Two methods for removing outliers are used in the program:
automatic (line 17) and manual (line 18). The latter opens an
interactive editor (see Fig. 5) which allows the user to select a
rectangular area defined by two points. The points included
in these areas can then be removed from data.
• In line 24, interpolated HR data inside and outside each
episode is compared. Function AnalyzeHRbyEpisodes() Fig. 6 – Plot obtained with function PlotHR().
 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50 45

Fig. 7 – Plot obtained with function PlotPowerBand().

• The power of the heart rate values in the spectral bands

ULF, VLF, LF and HF is estimated in line 29 and this informa-
tion is included in the frequency analysis created in line 28.
Arguments of CalculatePowerBand() control several para-
meters related to the windowing, spectrogram calculation,
and power spectral bands definition.
• Using episodic information to split frequency analysis is
also possible, as shown in lines 32 to 36. The output of these
lines of code is given in Listing 3. This example uses func-
tion t-test from the R package stats to perform a Student’s
t-test to the ULF band of segments before and after apnea
episodes.
4. A clinical example
As a clinical example of using the RHRV software package,
we present an analysis of a patient suffering from sleep
apnea. The example consists of data from a polysomnogram
with an ECG record and an ASCII file with annotations of
respiratory events, including obstructive apnea (OBSAPNEA),
hypoapnea (GENHYPO) and central apnea (CENAPNEA) epi-
sodes. Each episode was determined by an initial time and
duration, and contains information of oxygen saturation level
decreases. While based on real data, however, the purpose of

Listing 2 – Result of analyzing interpolated Heart Rate using episodes.

46 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Listing 3 – Result of analyzing power bands using episodes.
this example is merely to explain how our RHRV package could
be used for testing a hypothesis, and is not meant to suggest a
rigorous clinical procedure for experiments of sleep apnea and
ischaemia.
As was mentioned previously, HRV is a good indicator of
the status of the neurovegetative control system and, as such,
is a good non-invasive indicator of some pathologies. Its rela-
tion with sleep apnea has been established by several papers
[25–27]. Nonetheless, our analysis of the LF/HF ratio, which
is used as an indicator of balance between sympathetic and
parasympathetic systems, is not conclusive.
In this study, the RHRV software package was used to
calculate the LF/HF ratio for the ECG apnea events pre-
viously described: in particular for OBSAPNEA, GENHYPO, and
CENAPNEA. This was done in order to determine if statisti-
cal differences can be discerned from the three types of sleep
apnea classes. To do this with our software, the following steps
are required:
1. Create the data structure.
2. Load the heart beats and the apnea episodes from the
annotation file.
3. Estimate the non-interpolated heart rate (NIHR) frequency.
4. Reject artifacts with the automatic filter and manual edi-
ting.
5. Interpolate the heart rate signal at 4 Hz.
6. Create a data structure for the frequency analysis.
7. Perform a power spectral analysis using a Short-Time Fou-
rier Transform (STFT) with a window size of 30 seconds,
a displacement of 2.5 seconds and a zero-padding of 1024
samples. Next, the power spectra were calculated for each
spectral band (ULF, VLF, LF and HF), as well as the total
power spectrum. The LF/HF ratio was calculated for each
type of apneic events.
Table 1 – Differences in LF/HF ratios (R) for the three
types of apnea episodes, and corresponding 95%CIs.
OBSAPNEA GENHYPO
GENHYPO
R 0.152
95%CI (−0.331, 0.028)
CENAPNEA
R 0.816 0.969
95%CI (0.641, 0.991) (−1.108, −0.829)
The software implementation of these steps, using the
RHRV package, is given in Listing 4.
Results were evaluated employing a t-test that estimates
the 95% confidence intervals (95%CIs) and the p-value. Statis-
tically significant differences were obtained for the LF/HF ratio
for all the types of apnea episodes, which are given in Table 1.
A general statistical condition for two independent sets to be
significantly different, with respect to a given variable, is that
the variable does not assume a zero value within the corres-
ponding 95% confidence interval (CI) [28]. From this definition,
we found significant differences when comparing the CENAP-
NEA events with the GENHYPO and OBSAPNEA episodes. The
box-plot in Fig. 8 shows the average LF/HF ratios, quartiles,
maximum, and minimum obtained from power spectral ana-
lysis applied to the apnea episodes of the study.
This clinical example also illustrates other useful functions
of the RHRV software package. In particular, the software can
be used to compare the heart rate data prior-, or posterior-, to an
annotated apnea episode interval. Such a study could be useful
for searching for patterns or testing hypothesis of the origins
of apnea. For this task, we generated two new episodes: the
first was 5 minutes before the given OBSAPNEA apnea episode,
and the second was 5 minutes after the OBSAPNEA episode
(Listing 5). Once these new episodes have been established,
a new analysis was performed in the same way as descri-
 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50 47

Listing 4 – R file used for clinical experiment.

Listing 5 – Code implementation for generating episodes before and after the apnea events.

bed previously. The result of this analysis is that now we can

obtain LF/HF ratios 5 minutes before and after the OBSAPNEA
episode, which can be used for a statistical comparison. Our
results of this analysis are shown in Table 2.
A careful study of the results of Table 2, reveals that while
no important distinction exists between the posterior- signal as
compared with the apnea episode, there does exist a statistical
difference between the prior- episode as compared with the
apneic episode. While these results are suggestive, this is by
no means an exhaustive study, and is only meant to illustrate
the use of our software package.

Table 2 – Differences in LF/HF ratios (R) and 95%CIs for

before, during and after obstructive apnea episodes.
5 minutes before 5 minutes after
OBSAPNEA OBSAPNEA
OBSAPNEA
Fig. 8 – Average LF/HF ratios for the OBSAPNEA, GENHYPO R 0.206 0.095
and CENAPNEA episodes. 95%CI (0.043, 0.368) (−0.256, 0.066)
48 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Fig. 9 – Non-interpolated HR and spectrogram obtained with RHRV and matplotlib.
5. Discussion
We believe that the examples of the previous section demons-
trate both the adequacy and intuitive design of our R software
package for analyzing the heart rate variability. The soft-
ware package is easily downloaded and installed, following
standard procedures for third party software for the R plat-
form. Updates of our software are periodically uploaded to
the public R-CRAN repository, together with a detailed change
log. Moreover, the source code is completely available under
an open source license, allowing researchers to mold the tool
to their requirements.
Our data model with R offers a great degree of flexibility
for a wide spectrum of users. To make our package easier to
use, we have developed a web-service application [31] that is
capable of executing the application directly from a web brow-
ser, without the need to install software, as can be seen in
Fig. 10. This web interface could be useful for physicians that
desire results offered by our software, without having to install
the R environment. This service offers researchers the possibi-
lity of analyzing their own records in our server, obtain results,
visualize them and download numerical results in ASCII for-
mat. R users with modest programming skills can integrate
the data model and the RHRV functions into their own scripts,
as can be seen in the examples included in this paper. At the
other end of the spectrum, advanced users can easily modify
existing RHRV functions or add their own algorithms using our
data model, thereby making their functions compatible with
the entire RHRV library.
Using open source software offers a number of advantages
for integrating the package with other systems. As an example,
Fig. 9 shows a plot with data generated from our R package
and processed through matplotlib [30], which is a powerful
graphic library developed for python. The plot shows the non-
interpolated heart rate and the spectrogram (white lines mark
the limits of the ULF, VLF, LF and HF bands). Matplotlib is beco-
ming popular among scientists for its flexibility for producing
complex plots. This example demonstrates that while no spe-
cific bindings have been included yet into the R language for
matplotlib, the open design of our package permits unlimi-
ted possibilites for the user to combine the output with other
tools.
At present, our R package is being used in two Spanish
hospitals for heart rate variability analysis, specifically for
analyzing records from apneic patients. Results from recent
clinical studies, that we obtained by using our package, have
been accepted for publication, and will appear soon [29]. We
have also begun a study with the use of our package for ana-
lyzing patients with Chronic Obstructive Pulmonary disease.
While a stable version is presently being used in a hospital
setting and by other research groups, we are continually inclu-
ding improvements and new algorithms into the package. In
particular, the next major version of our software will include
in time domain and non-linear fractal dimension analysis.
 c o m p u t e r m e t h o d s a n d p r o g r a m s i n b i o m e d i c i n e 1 0 3 ( 2 0 1 1 ) 39–50
Fig. 10 – Integration of RHRV in a web application.
Acknowledgements
This work was supported by the Xunta de Galicia under the
grant 08SIN002206PR and the Spanish Ministry under the grant
TIN-2006-15460-C04-02.
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