Type:	Package
Title:	Filter Noisy Data
Version:	0.2
Date:	2023-05-24
Maintainer:	Thomas Ruf <Thomas.P.Ruf@me.com>
Description:	Noise filter based on determining the proportion of neighboring points. A false point will be rejected if it has only few neighbors, but accepted if the proportion of neighbors in a rectangular frame is high. The size of the rectangular frame as well as the cut-off value, i.e. of a minimum proportion of neighbor-points, may be supplied or can be calculated automatically. Originally designed for the cleaning of heart rates, but suitable for filtering any slowly-changing physiological variable.For more information see Signer (2010)<doi:10.1111/j.2041-210X.2009.00010.x>.
License:	GPL (≥ 3)
Encoding:	UTF-8
LazyData:	true
Imports:	ggplot2, gridExtra
Depends:	R (≥ 3.50)
Suggests:	knitr, rmarkdown
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2023-05-24 10:57:28 UTC; ruf
Author:	Thomas Ruf [aut, cre]
Repository:	CRAN
Date/Publication:	2023-05-24 11:20:11 UTC

Boxfilter Main Function

Description

Filters noise from data (e.g. heartrates) using x for x-axis data and y for y-axis, based on the proportion of neighbors of each point in a surrounding box of width and height (these may be determined automatically). It discards all data points that have less than a proportion of clipit neighbors.

Usage

boxclip (x=NULL,y,clipit=NULL,QI=NULL,width=NULL, height=NULL,
miny=min(y,na.rm=TRUE), maxy=max(y,na.rm=TRUE), plotit=TRUE, histo=FALSE)

Arguments

ci

Details

Boxfilter mimics the human criterion of self-similarity. Data points with many neighbors are more trustworthy.

Value

Note

To store only filtered data, use e.g.:

bc=boxclip (x,y) data=data.frame(x=bc$x, hrf=bc$filtered) data=na.omit(data) write.csv(data,file="myheartrates.csv")

Author(s)

Thomas Ruf (thomas.p.ruf@me.com)

See Also

clipview

Examples

data("wb_month")
data("ibex_hr")

x=wb_month$x
y=wb_month$hr


myclip=boxclip(x,y, histo=TRUE)
summary(myclip)

r=seq(1,28400,by=4) 
myclip=boxclip(ibex_hr$Time[r],ibex_hr$Heartrate[r],0.65)
summary(myclip)
#store(myclip)


data("sleepduration")
Date=as.POSIXct(sleepduration$Date)
Duration=as.numeric(sleepduration$Bedtime)
boxclip(Date,Duration,miny=0)

Get View Of Different clipit Values

Description

Gives a view of the original data, a histogram of the neighbors, and results of four values of clipit. The cutoff-values clipit are determined by a sequence of length .-

Usage

clipview (x=NULL,y,clipit=NULL,width=NULL, height=NULL,
miny=min(y,na.rm=TRUE), maxy=max(y,na.rm=TRUE),plotit=FALSE)

Arguments

Details

Note that a sequence is required for clipit here, while a scalar is required in boxclip().

Value

There is no return value.Six graphs are generated, original, histogram, and four for each value of clipit.

Author(s)

Thomas Ruf (thomas.p.ruf@me.com)

See Also

boxclip()

Examples

data("wb_year")


r=seq(1,54179,by=5)   

x=wb_year$x[r]
y=wb_year$y[r]

clipview(x,y,clipit=seq(0.2,0.5,0.1), miny=10)

One year of heart rates of a capricorn free-living in the alps.

Description

Heart rates were obtained using acoustic loggers in the rumen.

Usage

data("ibex_hr")

Format

A data frame with 28454 observations on the following 2 variables.

Time

datetime

Heartrate

in bpm

References

Signer, C., Ruf, T., & Arnold, W. (2011). Hypometabolism and basking: The strategies of Alpine ibex to endure harsh over‐wintering conditions. Functional Ecology, 25(3), 537-547.

Examples

data(ibex_hr)

Boxfilter function

Description

Shows a graph of the data and its change over time.Called by boxclip()

Usage

showdata(x,y)

Arguments

Details

Asks the user whether to continue or not.Continue only if you want points to be deleted

Author(s)

Thomas Ruf (thomas.p.ruf@me.com)

Examples

set.seed(1234)
y=runif(1000,20,30)
ix=sample(1:1000,50)
y[ix]=runif(50,60,70)
showdata(1:1000,y)

data centering around sleeop in a humam

Description

data on duration in bed

Usage

data("sleepduration")

Format

A data frame with 881 observations on the following 2 variables.

Date

a character vector

Bedtime

a character vector, convert to decimal number

Source

https://www.kaggle.com/datasets/danagerous/sleep-data

Examples

data(sleepduration)
## maybe str(sleepduration) ; plot(sleepduration) ...

Store data

Description

Stores original and filtered data.

Usage

store(object)

Arguments

Value

returns nothing

Author(s)

Thomas Ruf (thomas.p.ruf@me.com)

Examples

data ("wb_month.RData")

x=wb_month$x
y=wb_month$hr

myclip=boxclip(x,y,clipit=0.25,width=15)
summary(myclip)
store(myclip)

Summarize boxclip results

Description

Summary method for class boxclip.

Usage

## S3 method for class 'boxclip'
summary(object,...)

Arguments

Value

summary.boxclip prints the following items:

Author(s)

Thomas Ruf thomas.p.ruf@me.com

References

Signer (2010) <doi: 10.1111/j.2041-210X.2009.00010.x>

See Also

boxclip

Examples

data ("wb_month.RData")

x=wb_month$x
y=wb_month$hr

myclip=boxclip(x,y,clipit=0.25,width=15)
summary(myclip)

One month of heart rates and their quality in a wild boar. Quality was assessed by Star-Oddi, Island.

Description

Heart rates were obtained from DST centi- HRT, Star-Oddi, Gardabaer, Iceland.

Usage

data("wb_month")

Format

A data frame with 3720 observations on the following 3 variables.

x

x-axis, datetime

hr

y-axis, heart rate

QI

quality index (0-3) of the signal

Examples

data(wb_month)

One year of heart rates of a wild boar female.

Description

Heart rates were obtained from DST centi- HRT, Star-Oddi, Gardabaer, Iceland.

Usage

data("wb_year")

Format

A data frame with 3720 observations on the following 3 variables.

x

x-axis, datetime

y

y-axis, heart rate

References

Ruf, T., Vetter, S. G., Painer, J., Stalder, G., & Bieber, C. (2021). Atypical for northern ungulates, energy metabolism is lowest during summer in female wild boars (Sus scrofa). Scientific Reports, 11(1), 1-12.

Examples

data(wb_year)