Type:	Package
Title:	Heart Rate Turbulence Analysis
Version:	1.0.1
Date:	2021-06-17
BugReports:	https://github.com/VBlesius/RHRT/issues
Description:	Methods to scan RR interval data for Premature Ventricular Complexes (PVCs) and parameterise and plot the resulting Heart Rate Turbulence (HRT). The methodology of HRT analysis is based on the original publication by Schmidt et al. <doi:10.1016/S0140-6736(98)08428-1> and extended with suggestions from <doi:10.1088/1361-6579/ab98b3>.
Depends:	R (≥ 3.5.0)
License:	GPL-2
LazyData:	TRUE
Imports:	methods, graphics, utils
RoxygenNote:	7.1.1
Suggests:	knitr, rmarkdown, testthat, matrixStats
VignetteBuilder:	knitr
Collate:	'HRT.R' 'avHRT.R' 'HRTList.R' 'Testdata-description.R' 'constants.R' 'conversion_to_HRT.R' 'roll.R'
NeedsCompilation:	no
Packaged:	2021-06-28 08:48:40 UTC; blesius
Author:	Valeria Blesius [aut, cre]
Maintainer:	Valeria Blesius <valeria.blesius@mni.thm.de>
Repository:	CRAN
Date/Publication:	2021-06-29 06:00:02 UTC

S4 class to represent an HRT object

Description

This class specifies an object to save the lengths of intervals surrounding a premature ventricular beat. It saves the HRT parameters turbulence onset (TO), slope (TS) and timing (TT) after calculation as well as the coefficients of an ab-line used for the plot. TS is saved after common calculation and after normalising.

Usage

## S4 method for signature 'HRT'
initialize(
  .Object,
  couplRR = NA_real_,
  compRR = NA_real_,
  preRRs = NA_real_,
  postRRs = NA_real_
)

Arguments

Value

(HRT) A new HRT object

Slots

couplRR

(Numeric) Coupling interval

compRR

(Numeric) Compensatory interval

preRRs

(Numeric vector) Preceding intervals

postRRs

(Numeric vector) Following intervals

TO

(Numeric) Turbulence onset

TS

(Numeric) Turbulence slope

TT

(Numeric) Turbulence timing

intercept

(Numeric) Intercept of regression line of TS

nTS

(Numeric) Normalised Turbulence slope

nintercept

(Numeric) Intercept of regression line of nTS

S4 class to represent a list of HRT objects

Description

This class specifies an object to save all HRT objects of a given vector. It also saves an averaged HRT for calculation of the averaged HRT parameters and plotting of all HRTs in a single plot.

Usage

## S4 method for signature 'HRTList'
initialize(
  .Object,
  name = NA_character_,
  IL = NA_real_,
  pos = NA_real_,
  HRTs = list(),
  avHRT = new("avHRT"),
  RMSSD = NA_real_
)

Arguments

Value

(HRTList) A new HRTList object

Slots

name

(Character) Name of the vector if given

IL

(Numeric) Arithmetic mean of the overall interval length of the vector

pos

(Numeric vector) Positions of premature ventricular complexes in given input

HRTs

(List) All HRT objects

avHRT

(avHRT object) The average of all HRTs

RMSSD

(Numeric) Square root of the mean of the squared successive differences between adjacent intervals of the whole measurement

Note

After using vectorToHRT all slots in the resulting HRTList object are set. Please do not set them manually since many functions of the HRTList class rely on valid values assigned to the needed slots.

S4 class to represent an avHRT object

Description

This class extends the HRT class. An avHRT is the average of an HRTList and saves the way in which it was calculated.

Usage

## S4 method for signature 'avHRT'
initialize(
  .Object,
  av = mean,
  orTO = "avAfter",
  orTS = "avBefore",
  pTO = NA_real_,
  pTS = NA_real_,
  pTT = NA_real_,
  pnTS = NA_real_,
  nRMSSD = NA_real_,
  couplRR = NA_real_,
  compRR = NA_real_,
  preRRs = NA_real_,
  postRRs = NA_real_
)

Arguments

Value

(avHRT) A new avHRT object

Slots

av

(Function) Type of averaging, either mean or median

orTO

(Character) Order in which TO was calculated, either "avAfter" (assessment of parameter and averaging) or "avBefore" (averaging of the VPCSs and assessment of parameter)

orTS

(Character) Order in which TS was calculated, either "avAfter" (assessment of parameter and averaging) or "avBefore" (averaging of the VPCSs and assessment of parameter)

pTO

(Numeric) p-value of t-test checking the validity of TO

pTS

(Numeric) p-value of t-test checking the validity of TS

pTT

(Numeric) p-value of t-test checking the validity of TT

pnTS

(Numeric) p-value of t-test checking the validity of normalised TS

Calculate an avHRT object

Description

For each index the average of the intervals across all HRTs in the HRTList is calculated and the averaged HRT returned. The type of averaging, the order of HRT parameter assessment and interval lengths for normalising TS can be passed.

Usage

calcAvHRT(
  HRTListObj,
  av = mean,
  orTO = "avAfter",
  orTS = "avBefore",
  IL = HRTListObj@IL,
  normIL = c_normIL,
  normHallstrom = TRUE,
  coTO = COTO,
  coTS = COTS,
  coTT = COTT
)

## S4 method for signature 'HRTList'
calcAvHRT(
  HRTListObj,
  av = mean,
  orTO = "avAfter",
  orTS = "avBefore",
  IL = HRTListObj@IL,
  normIL = c_normIL,
  normHallstrom = TRUE,
  coTO = COTO,
  coTS = COTS,
  coTT = COTT
)

Arguments

Details

To eliminate other RR variability TS is commonly assessed after averaging the VPCSs. TO is commonly first calculated from the single VPCS and then averaged. (See 'Heart Rate Turbulence: Standards of Measurement, Physiological Interpretation, and Clinical Use, Axel Bauer et al., Journal of the American College of Cardiology, Volume 52, Issue 17, Pages 1353-1365')

Value

(avHRT) The avHRT object of the given HRTList

Examples

# You need an HRTList
hrtl <- vectorToHRT(testdataLong, testdataLong_Ann)

# Recalculate the avHRT with different normalisation
calcAvHRT(hrtl, normIL = 1000, normHallstrom = FALSE)

# Recalculate the avHRT based on a different calculation order
calcAvHRT(hrtl, orTO = "avBefore", orTS = "avAfter")

# Set custom parameter cut-offs for the reliability check
## You should keep in mind to give the same cut-offs when calling getResults()
calcAvHRT(hrtl, coTO = 0.022, coTS = 1.42, coTT = 12)

Calculate HRT parameters

Description

Calculates all HRT parameters needed for an HRT object and saves them in the corresponding slots.

Usage

calcHRTParams(HRTObj, IL = c_normIL, normIL = c_normIL)

## S4 method for signature 'HRT'
calcHRTParams(HRTObj, IL = c_normIL, normIL = c_normIL)

Arguments

Details

This method is a wrapper for the methods calcTO and calcTS.

Value

(HRT) An HRT object with (re)calculated HRT parameters

Calculate TO parameters

Description

Calculates the TO parameters and saves it in the corresponding slot

Usage

calcTO(HRTObj)

## S4 method for signature 'HRT'
calcTO(HRTObj)

Arguments

Value

(HRT) An HRT object with (re)calculated TO

Calculate TS parameters

Description

Calculates all TS parameters (TS itself, its index TT (turbulence timing) and the intercept for the plot) and saves them in the corresponding slots. Can also calculate normalised TS and intercept.

Usage

calcTS(HRTObj, normalising = FALSE, IL = c_normIL, normIL = c_normIL)

## S4 method for signature 'HRT'
calcTS(HRTObj, normalising = FALSE, IL = c_normIL, normIL = c_normIL)

Arguments

Value

(HRT) An HRT object with (re)calculated TS+intercept or nTS+nintercept

Checks annotations for compatibility

Description

Checks annotations for compatibility

Usage

checkAnnotations(annotations, input, PVCAnn, label)

Arguments

Value

No return value, possibly throws errors/warnings

Checks RR-intervals for HRT criteria and returns an HRT object

Description

Checks RR-intervals for HRT criteria and returns an HRT object

Usage

checkForHRT(intervals, numPreRRs = c_numPreRRs, numPostRRs = c_numPostRRs)

Arguments

Value

(HRT) A single HRT object

Checks data input for compatibility

Description

Checks data input for compatibility

Usage

checkInput(input, numSnippet, label)

Arguments

Value

No return value, possibly throws errors/warnings

Checks whether slots are set

Description

Checks whether slots are set

Check for HRTList class

Usage

checkValidity(x, ...)

## S4 method for signature 'HRT'
checkValidity(x)

## S4 method for signature 'HRTList'
checkValidity(x, av = FALSE, pos = FALSE)

Arguments

Value

No return value, possibly throws errors/warnings

No return value, possibly throws errors

Cleans data input for further checks or calculation

Description

Cleans data input for further checks or calculation

Usage

cleanInput(input)

Arguments

Value

(numeric vector) Input vector without possible bias

Extracts all values of a special slot out of a HRTList

Description

Extracts all values of the given slot in each HRT of the HRTList and returns them in a list

Usage

getHRTParams(HRTListObj, sl)

## S4 method for signature 'HRTList'
getHRTParams(HRTListObj, sl)

Arguments

Value

(numeric vector or list) Vector or list of the numerics stored in the given slot

Examples

# You need an HRTList
hrtl <- vectorToHRT(testdataLong, testdataLong_Ann)

# Get all TOs of the HRTs in your HRTList
getHRTParams(hrtl, "TO")

# You can access all slots in the HRTs
getHRTParams(hrtl, "intercept")

# If you access slots that include more than one numeric, the function returns a list
getHRTParams(hrtl, "preRRs")

Finds HRTs

Description

Scans for HRTs in the given vector and returns an HRTList object.

Usage

getHRTs(
  intervals,
  annotations = NULL,
  PVCAnn = "V",
  numPreRRs = c_numPreRRs,
  numPostRRs = c_numPostRRs,
  numSnippet
)

Arguments

Value

(HRTList) HRTList with only pos and HRTs set

Get positions of PVCs

Description

Returns the positions of all ventricular premature complexes (VPCs) and accordingly the coupling intervals that were found in the given vector when the HRTList was created.

Usage

getPositions(HRTListObj)

## S4 method for signature 'HRTList'
getPositions(HRTListObj)

Arguments

Value

No return value, possibly throws errors/warnings

Returns the VPCS intervals in right order

Description

Returns the VPCS intervals in right order

Usage

getRRs(HRTObj)

## S4 method for signature 'HRT'
getRRs(HRTObj)

Arguments

Value

(numeric vector) All VPCS intervals

Get averaged HRT parameters

Description

Returns the HRT parameters of the HRTList. Turbulence onset is calculated for each HRT object and then averaged, turbulence slope is calculated via averaging the intervals of all HRT objects to one HRT object and then estimating the maximal slope.

Usage

getResults(
  HRTListObj,
  type = "class",
  TT = FALSE,
  nTS = FALSE,
  safe = TRUE,
  pmax = 0.05,
  num = FALSE,
  coTO = COTO,
  coTS = COTS,
  coTT = COTT
)

## S4 method for signature 'HRTList'
getResults(
  HRTListObj,
  type = "class",
  TT = FALSE,
  nTS = FALSE,
  safe = TRUE,
  pmax = 0.05,
  num = FALSE,
  coTO = COTO,
  coTS = COTS,
  coTT = COTT
)

Arguments

Value

(Named vector, character or numeric) Either HRT classes, HRT parameter values and/or p-values

Examples

# You need an HRTList
hrtl <- vectorToHRT(testdataLong, testdataLong_Ann)

# Get the HRT classes of your HRTList
getResults(hrtl)
getResults(hrtl, TT = TRUE)

# Get the HRT parameter values of your HRTList
getResults(hrtl, type = "parameter", TT = TRUE)

Plot an HRT object

Description

Plots RR-intervals saved in the HRT object and marks turbulence onset and turbulence slope.

Usage

## S4 method for signature 'HRT'
plot(
  x,
  cropped = TRUE,
  TT = FALSE,
  pch = 20,
  xlab = "# of RR interval",
  ylab = "length of RR interval (ms)",
  paramsLegend = TRUE,
  colTO = "#ec2023",
  colTS = "#006AFF",
  colTT = "#6800DE",
  add = FALSE,
  ...
)

Arguments

Value

No return value

Note

Please note that some graphics parameters (par) cannot be modified, since they are needed to be set inside the function.

Examples

# You need an HRT object
hrt <- vectorToHRT(testdataLong, testdataLong_Ann)@HRTs[[1]]

# Plot your HRT and zoom out
plot(hrt, cropped = FALSE)

# Include TT and customise it
plot(hrt, TT = TRUE, colTT = "green", pch = 7)

# Use standard graphics parameters
## Note: Some parameters are used inside the function and cannot be set
plot(hrt, TT = TRUE, main = "Example plot", bty = "n", cex.lab = 1.2)

Plot an HRTList object

Description

Plots RR-intervals saved in the HRT objects, especially the avHRT object, and marks the HRT parameters.

Usage

## S4 method for signature 'HRTList'
plot(
  x,
  cropped = TRUE,
  TT = FALSE,
  pch = 20,
  xlab = "# of RR interval",
  ylab = "length of RR interval (ms)",
  paramsLegend = TRUE,
  colTO = "#ec2023",
  colTS = "#006AFF",
  colTT = "#6800DE",
  ...
)

Arguments

Value

No return value

Note

Please note that some graphics parameters (par) cannot be modified, since they are needed to be set inside the function.

Examples

# You need an HRTList
hrtl <- vectorToHRT(testdataLong, testdataLong_Ann)

# Plot your HRTList and zoom out
plot(hrtl, cropped = FALSE)

# Include TT and customise it
plot(hrtl, TT = TRUE, colTT = "green", pch = 7)

# Use standard graphics parameters
## Note: Some parameters are used inside the function and cannot be set
plot(hrtl, TT = TRUE, main = "Example plot", bty = "n", cex.lab = 1.2)

Apply method on sliding window

Description

Applies a given function on a vector by rolling over it with a sliding window mechanism.

Usage

roll(intervals, width, fun, ...)

Arguments

Details

This method was inspired by the function "wapply" by A. N. Spiess, University Hospital Hamburg-Eppendorf (https://rmazing.wordpress.com/2013/04/23/wapply-a-faster-but-less-functional-rollapply-for-vector-setups/), but adjusted for this package to speed it up.

Value

(list) List with return values of fun for each window

Long term data

Description

Artificial dummy interval data: This dataset represents a long-term measurement and includes 15 VPCSs that fit the HRT filter rules.

Usage

testdataLong

Format

A numeric vector.

Long term data annotations

Description

Artificial dummy interval data: This dataset contains the annotations matching testdataLong.

Usage

testdataLong_Ann

Format

A vector of characters.

Convert a vector to HRTList

Description

Scans for heart rate turbulence in a vector of RR-intervals and returns an HRTList object including all found HRT objects. The HRT criteria used were published by Schmidt et al. (more information can be found in the vignette.)

Usage

vectorToHRT(
  input,
  annotations = NULL,
  PVCAnn = "V",
  normIL = c_normIL,
  normHallstrom = TRUE,
  numPreRRs = c_numPreRRs,
  numPostRRs = c_numPostRRs,
  inputName = as.character(NA),
  minHRT = 5,
  cleaning = TRUE
)

Arguments

Value

(HRTList) An HRTList object

Examples

# You can use annotations to give the VPC indices
# Without annotation data RHRT will find VPCs based on common filtering criteria
vectorToHRT(testdataLong, annotations = testdataLong_Ann, PVCAnn = "V")

# Find HRTs with a broader range of sinus beats before and after the VPCs
vectorToHRT(testdataLong, inputName = "Dummy Measurement", numPreRRs = 10, numPostRRs = 20)
 
# Adjust the normalisation parameters
vectorToHRT(testdataLong, testdataLong_Ann, normHallstrom = FALSE, normIL = 900)