NOTE: If you are viewing this page via CRAN note that additional documentation can be found in the GGIR GitHub pages.
If you like GGIR but want to use algorithms for raw data not included in GGIR then the external function embedding feature can be the solution. For example, you may want to pilot a new machine learned classifiction algorithm but you do not want to write all the data cleaning and aggregation steps needed for analysis of real life ‘out of the lab’ acceleormeter data.
How it works:
Internally GGIR loads the raw accelerometer data in memory blocks of about 24 hours. When the data is in memory, corrected for calibration error, and resampled to the sample rate required by your function, GGIR applies its own default algorithms as well as the external function provided by you (Python or R). The external function is expected to take as input: A three-column matrix with the acceleration data corresponding to the three acceleration axes, and an optional parameters argument which can be of any R format (character, list, vector, data.frame, etc). As output your external function is expected to produce a matrix or data.frame with one or multiple columns corresponding to the output of your external function.
In this example we will apply the function counts() from R package activityCounts to the raw data, which produces an estimate of Actigraph counts per second.
Create file calculateCounts.R and insert the following code:
calculateCounts = function(data=c(), parameters=c()) {
# data: 3 column matrix with acc data
# parameters: the sample rate of data
library("activityCounts")
if (ncol(data) == 4) data= data[,2:4]
mycounts = counts(data=data, hertz=parameters,
x_axis=1, y_axis=2, z_axis=3,
start_time = Sys.time())
mycounts = mycounts[,2:4] #Note: do not provide timestamps to GGIR
return(mycounts)
}Create a new .R file for running the GGIR analysis, e.g. named
myscript.R, and insert the following code. Do not forget to
update the filepath on the first line to point to your
calculateCounts.R file.
source("~/calculateCounts.R")
myfun = list(FUN=calculateCounts,
parameters= 30,
expected_sample_rate= 30,
expected_unit="g",
colnames = c("countsX","countsY","countsZ"),
outputres = 1,
minlength = 1,
outputtype="numeric",
aggfunction = sum,
timestamp=F,
reporttype="scalar")The above code creates object myfun of type
list which is expected to come with the following
elements:
FUN A character string specifying the location of the
external function you want to apply.parameters The parameters used by the function, which
can be stored in any format (vector, matrix, list, data.frame). The user
should make sure that the external function can handle this object.expected_sample_rate Expected sample rate, if the
inputdata has a difference sample rate, then the data will be
resampled.expected_unit Expected unit of the acceleration by
external function: “mg”, “g” or “ms2”. If input data is different it
will be converted.colnames Character vector with the names of the columns
produced by the external function.outputres The resolution (seconds) of the output
produced by the external function. Note, that this needs to be equal to
or a multitude of the short epoch size of the g.part1 output (5 seconds)
or the short epoch size should be a multitude of this resolution. In
this way GGIR can aggregate or repeat the external function output to be
used inside GGIR.minlength The minimum length (seconds) of input data
needed, typically the window per which output is provided.outputtype Character to indicate the type of external
function output. Set to “numeric” if data is stored in numbers (any
numeric format), or “character” if it is a character string.aggfunction If the data needs to be aggregated to match
the short epoch size of the g.part1 output (5 seconds) then this element
specifies what function should be used for the aggregation, e.g. mean,
sum, median.timestamp Boolean to indicated whether timestamps
(seconds since 1-1-1970) should be passed on to the external function as
first columm of the data matrix..reporttype Character to indicate the type of reporting
by GGIR: “scalar” if it should be averaged per day, “event” if it should
be summed per day, or “type” if it is categorical variable that can only
be aggregated per day by tabulating it.Next, add a call to GGIR function GGIR with myfun
provided as one of its arguments:
library(GGIR)
GGIR(datadir="~/myaccelerometerdata",
outputdir="~/myresults",
mode=1:2,
epochvalues2csv = TRUE,
do.report=2,
myfun=myfun) #<= this is where object myfun is provided to GGIRIn this example we will use an external Python function to estimate the dominant signal frequency per acceleration axis. Note this can also be done in R, but it shows that even Python functions can be provided.
Create dominant_frequency.py and insert the code shown below:
import numpy
def dominant_frequency(x, sf):
# x: vector with data values
# sf: sample frequency
fourier = numpy.fft.fft(x)
frequencies = numpy.fft.fftfreq(len(x), 1/sf)
magnitudes = abs(fourier[numpy.where(frequencies > 0)])
peak_frequency = frequencies[numpy.argmax(magnitudes)]
return peak_frequencyCreate dominant_frequency.R that calls the python function and insert the following code:
dominant_frequency = function(data=c(), parameters=c()) {
# data: 3 column matrix with acc data
# parameters: the sample rate of data
source_python("dominant_frequency.py")
sf=parameters
N = nrow(data)
ws = 5 # windowsize
if (ncol(data) == 4) data= data[,2:4]
data = data.frame(t= floor(seq(0,(N-1)/sf,by=1/sf)/ws),
x=data[,1], y=data[,2], z=data[,3])
df = aggregate(data, by = list(data$t),
FUN=function(x) {return(dominant_frequency(x,sf))})
df = df[,-c(1:2)]
return(df)
}
}Create a new .R file for running the GGIR analysis, e.g. named myscript.R, and insert the following blocks of code.
Specification of Python environment to use, this can also be a conda
environment or docker container (see documentation R package for further details).
Make sure that that this Python environment has all the required
dependencies for the external function, here we will only need
numpy.
library("reticulate")
use_virtualenv("~/myvenv", required = TRUE) # Local Python environment
py_install("numpy", pip = TRUE)Specify a myfun object as explained in the R example. Do
not forget to update the filepath to the
"~/dominant_frequency.R" file.
source("~/dominant_frequency.R")
myfun = list(FUN=dominant_frequency,
parameters= 30,
expected_sample_rate= 30,
expected_unit="g",
colnames = c("domfreqX", "domfreqY", "domfreqZ"),
minlength = 5,
outputres = 5,
outputtype="numeric",
aggfunction = median
timestamp=F,
reporttype="scalar")Add a call to function GGIR where myfun is provided as
argument. Note that, do.parallel is set to FALSE. Unfortunately Python
embedding with R package reticulate and multi-threading with R package
foreach as used in GGIR do not combine well.
library(GGIR)
GGIR(datadir="~/myaccelerometerdata",
outputdir="~/myresults",
mode=1:2,
epochvalues2csv = TRUE,
do.report=2,
myfun=myfun,
do.parallel = FALSE)The external function output is included in the time series produced
by function GGIR function g.part1 and stored in an RData-file in
/output_nameofstudy/meta/basic. The resolution of these
output in GGIR is set by GGIR argument windowsizes, which
is c(5,900,3600) by default. Here, the first element
5 specifies the short epoch size in seconds. If the output
of the external function is less then this resolution it will be
aggregated with the function as specificied by aggfunction in the
myfun object. In the count example we used the sum for this
and for the dominant frequency example we used the median.
Next, in part2 GGIR aims to detect non-wear periods and imputes
those. The impute time series can be found in the part 2 milestone data
in folder: /output_nameofstudy/meta/ms2.out. If you want
these to be directly stored in a csv file then set argument
epochvalues2csv = TRUE.