read.myacc.csv {GGIR}

Read custom csv files with accelerometer data

Description

Loads csv files with accelerometer data and standardises the output format (incl. unit of measurement, timestamp format, header format, and column locations) to make the data compatible with other GGIR functions.

Usage

  read.myacc.csv(rmc.file=c(), rmc.nrow=Inf, rmc.skip = c(), rmc.dec=".",
                          rmc.firstrow.acc = c(), rmc.firstrow.header=c(),
                          rmc.header.length = c(),
                          rmc.col.acc = 1:3, rmc.col.temp = c(), 
                          rmc.col.time=c(),
                          rmc.unit.acc = "g", rmc.unit.temp = "C", 
                          rmc.unit.time = "POSIX",
                          rmc.format.time = "%Y-%m-%d %H:%M:%OS",
                          rmc.bitrate = c(), rmc.dynamic_range = c(), 
                          rmc.unsignedbit = TRUE,
                          rmc.origin = "1970-01-01",
                          rmc.desiredtz = NULL,
                          rmc.configtz = NULL,
                          rmc.sf = c(),
                          rmc.headername.sf = c(),
                          rmc.headername.sn = c(),
                          rmc.headername.recordingid = c(),
                          rmc.header.structure = c(),
                          rmc.check4timegaps = FALSE,
                          rmc.col.wear = c(),
                          rmc.doresample = FALSE,
                          rmc.scalefactor.acc = 1,
                          interpolationType=1, 
                          PreviousLastValue = c(0, 0, 1),
                          PreviousLastTime = NULL,
                          desiredtz = NULL,
                          configtz = NULL,
                          header = NULL)	

Arguments

rmc.file

Filename of file to be read if it is in the working directory, or full path to the file otherwise.

rmc.nrow

Number of rows to read, same as nrow argument in read.csv and nrows in fread. The whole file is read by default (i.e., rmc.nrow = Inf).

rmc.skip

Number of rows to skip, same as skip argument in read.csv and in fread.

rmc.dec

Decimal used for numbers, same as skip argument in read.csv and in fread.

rmc.firstrow.acc

First row (number) of the acceleration data.

rmc.firstrow.header

First row (number) of the header. Leave blank if the file does not have a header.

rmc.header.length

If file has header, specify header length (numeric).

rmc.col.acc

Vector with three column (numbers) in which the acceleration signals are stored

rmc.col.temp

Scalar with column (number) in which the temperature is stored. Leave in default setting if no temperature is avaible. The temperature will be used by g.calibrate.

rmc.col.time

Scalar with column (number) in which the timestamps are stored. Leave in default setting if timestamps are not stored.

rmc.unit.acc

Character with unit of acceleration values: "g", "mg", or "bit"

rmc.unit.temp

Character with unit of temperature values: (K)elvin, (C)elsius, or (F)ahrenheit

rmc.unit.time

Character with unit of timestamps: "POSIX", "UNIXsec" (seconds since origin, see argument rmc.origin), "character", or "ActivPAL" (exotic timestamp format only used in the ActivPAL activity monitor).

rmc.format.time

Character string giving a date-time format as used by strptime. Only used for rmc.unit.time: character and POSIX.

rmc.bitrate

Numeric: If unit of acceleration is a bit then provide bit rate, e.g. 12 bit.

rmc.dynamic_range

Numeric, if unit of acceleration is a bit then provide dynamic range deviation in g from zero, e.g. +/-6g would mean this argument needs to be 6. If you give this argument a character value the code will search the file header for elements with a name equal to the character value and use the corresponding numeric value next to it as dynamic range.

rmc.unsignedbit

Boolean, if unsignedbit = TRUE means that bits are only positive numbers. if unsignedbit = FALSE then bits are both positive and negative.

rmc.origin

Origin of time when unit of time is UNIXsec, e.g. 1970-1-1

rmc.desiredtz

Deprecated, please see desiredtz.

rmc.configtz

Deprecated, please see configtz.

rmc.sf

Sample rate in Hertz, if this is stored in the file header then that will be used instead.

rmc.headername.sf

If file has a header: Row name (character) under which the sample frequency can be found.

rmc.headername.sn

If file has a header: Row name (character) under which the serial number can be found.

rmc.headername.recordingid

If file has a header: Row name (character) under which the recording ID can be found.

rmc.header.structure

Character used to split the header name from the header value, e.g. ":" or " "

rmc.check4timegaps

Boolean to indicate whether gaps in time should be imputed with zeros. Some sensing equipment provides accelerometer with gaps in time. The rest of GGIR is not designed for this, by setting this argument to TRUE the the gaps in time will be filled with zeros.

rmc.col.wear

If external wear detection outcome is stored as part of the data then this can be used by GGIR. This argument specifies the column in which the wear detection (Boolean) is stored.

rmc.doresample

Boolean to indicate whether to resample the data based on the available timestamps and extracted sample rate from the file header

rmc.scalefactor.acc

Numeric value (default 1) to scale the acceleration signals via multiplication. For example, if data is provided in m/s2 then by setting this to 1/9.81 we would derive gravitational units.

interpolationType

Integer to indicate type of interpolation to be used when resampling time series (mainly relevant for Axivity sensors), 1=linear, 2=nearest neighbour.

PreviousLastValue

Automatically identified last value in previous chunk of data read.

PreviousLastTime

Automatically identified last timestamp in previous chunk of data read.

desiredtz

Timezone in which device was worn.

configtz

Timezone in which device was configured. If equal to desiredtz you can leave this in its default value.

header

Header information that was extracted the previous time this file was read, to be re-used instead of being extracted again.

Details

To use this function in the context of GGIR use all arguments from this function, except rmc.file, rmc.nrow, and rmc.skip as input for function GGIR or g.part1 and also specify argument rmc.noise, which is not part of this function but needed to tell GGIR what noise level to expect in the data. The rmc.noise is taken from the params_rawdata object if not explicitly specified by user.

Value

List with objects data holding the time series of acceleration, and header if it was available in the orignal file.

Author(s)

Vincent T van Hees <[e-mail]>

Examples

  # create test files: No header, with temperature, with time
  N = 30
  sf = 30
  x = Sys.time()+((0:(N-1))/sf)
  timestamps = as.POSIXlt(x, origin="1970-1-1", tz = "Europe/London")
  mydata = data.frame(x = rnorm(N), time = timestamps, y = rnorm(N), z = rnorm(N),
            temp = rnorm(N) + 20)
  testfile = "testcsv1.csv"
  write.csv(mydata, file= testfile, row.names = FALSE)
  loadedData = read.myacc.csv(rmc.file=testfile, rmc.nrow=20, rmc.dec=".",
                      rmc.firstrow.acc = 1, rmc.firstrow.header=c(),
                      desiredtz = "",
                      rmc.col.acc = c(1,3,4), rmc.col.temp = 5, rmc.col.time=2,
                      rmc.unit.acc = "g", rmc.unit.temp = "C", rmc.origin = "1970-01-01")
  if (file.exists(testfile)) file.remove(testfile)