| collapse.accfile {pawacc} | R Documentation |
Collapse raw accelerometer files into a summary dataset
Description
This function collapses accelerometer data into a dataframe with summary statistics.
Usage
collapse(...)
## S3 method for class 'accfile'
collapse(object, which = "counts", palist = list(value = c(0, 100, 1000, 5000, 13000),
rescale.epoch = 60, labels = NULL, extreme = NULL), mwlist = list(value = 20,
nz = 0, rescale.epoch = 60), collapse.by = "%Y-%m-%d", collapse.epoch = 60, aggregate.by =
NULL, FUN.list = list(mean = function(x) mean(x, na.rm = TRUE)),
keep.extreme = FALSE, keep.error = FALSE, ...)
Arguments
object |
an object of class |
which |
either 'counts' or 'steps' for |
palist |
list of arguments for |
mwlist |
list of arguments for |
collapse.by |
dataset aggregation level. See argument |
collapse.epoch |
epoch by which time spent in different physical activity modes is summarized. See details. |
aggregate.by |
pre-collapsing aggregation level for accelerometer values. See argument |
FUN.list |
a named list of functions. See |
keep.extreme |
logical flag. If |
keep.error |
logical flag. If |
... |
arguments for |
Value
A data frame containing the following variables
collapse.by |
aggregation factor |
fileid |
file identifier |
... |
named columns according to arguments |
Author(s)
Marco Geraci
References
Geraci M, Rich C, Sera F, Cortina-Borja M, Griffiths LJ, and Dezateux C (2012). Technical report on accelerometry data processing in the Millennium Cohort Study. London, UK: University College London. Available at https://discovery.ucl.ac.uk/1361699
See Also
markpa.accfile, markwear.accfile, fun.collapse
Examples
## Not run:
data(gt1m_sample)
collapse(gt1m_sample, palist = list(value = c(0, 100, 2000, 4000, 11000),
rescale.epoch = 60, labels = c("sedentary","light","moderate","vigorous","extreme_values"),
extreme = "last"), mwlist = list(value = 20,
nz = 0), collapse.by = "%Y-%m-%d", collapse.epoch = 60,
FUN.list = list(mean = function(x) round(mean(x, na.rm = TRUE),2)),
keep.extreme = FALSE, keep.error = FALSE)
$outcome
collapse.by fileid outcome.mean sedentary light moderate vigorous
1 2011-12-08 test 117.63 293.75 243.75 29.75 4.00
2 2011-12-09 test 157.83 349.75 143.25 33.50 24.50
3 2011-12-10 test 79.75 468.25 177.25 24.25 6.25
4 2011-12-11 test 57.96 355.50 126.00 8.50 3.25
5 2011-12-12 test 70.05 455.50 157.25 19.50 6.00
6 2011-12-13 test 72.99 475.50 181.50 15.25 8.00
7 2011-12-14 test 79.94 476.25 210.50 20.25 8.50
8 2011-12-15 test 232.50 0.00 0.50 0.00 0.00
9 2011-12-16 test NaN 0.00 0.00 0.00 0.00
extreme_values non-wear
1 0.00 388.75
2 6.00 883.00
3 0.50 763.50
4 0.25 946.50
5 0.00 801.75
6 0.25 759.50
7 1.50 723.00
8 0.00 1439.50
9 0.00 187.50
$call
collapse.accfile(object = gt1m_sample, palist = list(value = c(0,
100, 2000, 4000, 11000), rescale.epoch = 60, labels = c("sedentary",
"light", "moderate", "vigorous", "extreme_values"), extreme = "last"),
mwlist = list(value = 20, nz = 0), collapse.by = "
collapse.epoch = 60, FUN.list = list(mean = function(x) round(mean(x,
na.rm = TRUE), 2)), keep.extreme = FALSE, keep.error = FALSE)
attr(,"class")
[1] "accfile.collapse"
Warning message:
In collapse.accfile(gt1m_sample, palist = list(value = c(0, 100, :
NAs imputed where extreme counts found
## End(Not run)
## Not run:
collapse(gt1m_sample, palist = list(value = c(0, 100, 2000, 4000, 11000),
rescale.epoch = 60, labels = c("sedentary","light","moderate","vigorous","extreme_values"),
extreme = "last"), mwlist = list(value = 20,
nz = 0), collapse.by = "%Y-%m-%d", collapse.epoch = 60,
FUN.list = list(mean = function(x) round(mean(x, na.rm = TRUE),2),
sd = function(x) round(sd(x, na.rm = TRUE),2),
"95th" = function(x) round(quantile(x, probs = .95, na.rm = TRUE),2)),
keep.extreme = TRUE, keep.error = FALSE)
$outcome
collapse.by fileid outcome.mean outcome.sd outcome.95th sedentary light
1 2011-12-08 test 117.63 216.12 529.40 293.75 243.75
2 2011-12-09 test 201.10 567.65 1085.60 349.75 143.25
3 2011-12-10 test 81.97 221.33 465.50 468.25 177.25
4 2011-12-11 test 59.80 172.08 320.35 355.50 126.00
5 2011-12-12 test 70.05 188.49 401.00 455.50 157.25
6 2011-12-13 test 74.08 207.55 386.85 475.50 181.50
7 2011-12-14 test 87.42 275.27 415.30 476.25 210.50
8 2011-12-15 test 232.50 222.74 374.25 0.00 0.50
9 2011-12-16 test NaN NA NA 0.00 0.00
moderate vigorous extreme_values non-wear
1 29.75 4.00 0.00 388.75
2 33.50 24.50 6.00 883.00
3 24.25 6.25 0.50 763.50
4 8.50 3.25 0.25 946.50
5 19.50 6.00 0.00 801.75
6 15.25 8.00 0.25 759.50
7 20.25 8.50 1.50 723.00
8 0.00 0.00 0.00 1439.50
9 0.00 0.00 0.00 187.50
$call
collapse.accfile(object = gt1m_sample, palist = list(value = c(0,
100, 2000, 4000, 11000), rescale.epoch = 60, labels = c("sedentary",
"light", "moderate", "vigorous", "extreme_values"), extreme = "last"),
mwlist = list(value = 20, nz = 0), collapse.by = "
collapse.epoch = 60, FUN.list = list(mean = function(x) round(mean(x,
na.rm = TRUE), 2), sd = function(x) round(sd(x, na.rm = TRUE),
2), `95th` = function(x) round(quantile(x, probs = 0.95,
na.rm = TRUE), 2)), keep.extreme = TRUE, keep.error = FALSE)
attr(,"class")
[1] "accfile.collapse"
## End(Not run)