Flag Spikes
Usage
flag_spike(df, spike_size = 11)
flag_interval_jump(df, verbose = FALSE)
flag_spike_second(df, spike_size = 11)
flag_device_limit(df, dynamic_range = NULL, epsilon = 0.05)
flag_contiguous_device_limit(df, dynamic_range = NULL, epsilon = 0.05)
flag_same_value(df, min_length = 1)
flag_all_zero(df, min_length = 3)
flag_impossible(df, min_length = 6)Arguments
- df
A data set of actigraphy
- spike_size
size of "spike" - which is the absolute difference in contiguous observations on a single axis
- verbose
print diagnostic messages
- dynamic_range
dynamic range of the device, used to find the device limit.
- epsilon
A small adjustment so that if values are within the device limit, but minus epsilon, still flagged as hitting the limit. For example, if `dynamic_range = c(-6, 6)` and `epsilon = 0.05`, then any value <= `-5.95` or `>= 5.95` gravity units will be flagged
- min_length
minimum length of the condition for contiguous samples. If `min_length = 3`, then at least 3 `TRUE`s in a row is required, any stretches of single `TRUE` values or 2 `TRUE` followed by `FALSE`, will be set to `FALSE`.
Note
`flag_spike` looks if 2 contiguous values, within each axis, are larger than a absolute size (`11` gravity units). The `flag_spike_second` function groups the data by second, finds the range of values, within each axis, and determines if this range is greater than a specified size (`11` g).
Examples
file = system.file("extdata", "TAS1H30182785_2019-09-17.gt3x",
package = "SummarizedActigraphy")
res = read_actigraphy(file)
#> Input is a .gt3x file, unzipping to a temporary location first...
#> Unzipping gt3x data to /tmp/RtmpsiCePd
#> 1/1
#> Unzipping /home/runner/work/_temp/Library/SummarizedActigraphy/extdata/TAS1H30182785_2019-09-17.gt3x
#> === info.txt, log.bin extracted to /tmp/RtmpsiCePd/TAS1H30182785_2019-09-17
#> GT3X information
#> $ Serial Number :"TAS1H30182785"
#> $ Device Type :"Link"
#> $ Firmware :"1.7.2"
#> $ Battery Voltage :"4.18"
#> $ Sample Rate :100
#> $ Start Date : POSIXct, format: "2019-09-17 18:40:00"
#> $ Stop Date : POSIXct, format: "2019-09-18 19:00:00"
#> $ Last Sample Time : POSIXct, format: "2019-09-17 19:20:05"
#> $ TimeZone :"-04:00:00"
#> $ Download Date : POSIXct, format: "2019-09-17 19:20:05"
#> $ Board Revision :"8"
#> $ Unexpected Resets :"0"
#> $ Acceleration Scale:256
#> $ Acceleration Min :"-8.0"
#> $ Acceleration Max :"8.0"
#> $ Subject Name :"suffix_85"
#> $ Serial Prefix :"TAS"
#> Parsing GT3X data via CPP.. expected sample size: 240500
#> ---GT3X PARAMETERS
#> address: 0 key: 6 value: 1
#> address: 0 key: 7 value: 54703161
#> address: 0 key: 8 value: 8
#> address: 0 key: 9 value: 1534154836
#> address: 0 key: 13 value: 17235970
#> address: 0 key: 16 value: 3791650816
#> address: 0 key: 20 value: 0
#> address: 0 key: 21 value: 0
#> address: 0 key: 22 value: 0
#> address: 0 key: 23 value: 0
#> address: 0 key: 26 value: 2
#> address: 0 key: 28 value: 262013
#> address: 0 key: 29 value: 255
#> address: 0 key: 32 value: 16908288
#> address: 0 key: 37 value: 1024
#> address: 0 key: 38 value: 0
#> address: 0 key: 49 value: 2048
#> address: 0 key: 50 value: 88181047
#> address: 0 key: 51 value: 6.82667
#> address: 0 key: 55 value: 256
#> address: 0 key: 57 value: 333.87
#> address: 0 key: 58 value: 21
#> address: 0 key: 61 value: 2
#> address: 1 key: 0 value: 0
#> address: 1 key: 1 value: 872668711
#> address: 1 key: 2 (features) value: 388
#> address: 1 key: 3 value: 1
#> address: 1 key: 4 value: 4294967131
#> address: 1 key: 5 value: 4294967095
#> address: 1 key: 6 value: 4294967149
#> address: 1 key: 7 value: 298
#> address: 1 key: 8 value: 286
#> address: 1 key: 9 value: 300
#> address: 1 key: 10 value: 100
#> address: 1 key: 12 (start time) value: 1568745600
#> address: 1 key: 13 value: 1568833200
#> address: 1 key: 14 value: 1568745556
#> address: 1 key: 15 value: 74
#> address: 1 key: 16 value: 40
#> address: 1 key: 17 value: 72
#> address: 1 key: 20 value: 0
#> address: 1 key: 21 value: 0
#> address: 1 key: 33 value: 60000
#> address: 1 key: 34 value: 4294965247
#> address: 1 key: 35 value: 4294965190
#> address: 1 key: 36 value: 4294965237
#> address: 1 key: 37 value: 2051
#> address: 1 key: 38 value: 2000
#> address: 1 key: 39 value: 2048
#> address: 1 key: 40 value: 0
#> address: 1 key: 41 value: 1
#> address: 1 key: 42 value: 0
#> address: 1 key: 43 value: 4294967283
#> address: 1 key: 44 value: 0
#> address: 1 key: 45 value: 0
#> address: 1 key: 46 value: 0
#> ---END PARAMETERS
#>
#> Activity with Sample Size of 0
#> payload start: 1568747741
#> total_records: 214100
#> max_samples: 240500
#> Activity with Sample Size of 0
#> payload start: 1568747759
#> total_records: 215900
#> max_samples: 240500
#> Total Records: 216000
#> Scaling...
#> Creating dimnames
#> CPP returning
#> Done (in 0.50003457069397 seconds)
res = flag_spike(res)
res = flag_interval_jump(res)
res = flag_spike_second(res)
res = flag_same_value(res)
res = flag_device_limit(res)
res = flag_all_zero(res)
res = flag_impossible(res)