collapse.accfile: Collapse raw accelerometer files into a summary dataset

Description

This function collapses Actigraph GT1M accelerometer files into a dataframe with summary statistics.

Usage

collapse.accfile(object, palist = list(value = c(0, 100, 1000, 5000, 13000),
rescale.epoch = 60, labels = NULL, extreme = NULL), mwlist = list(value = 20,
nz = 0), 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 gt1m.

palist

list of arguments for markpa.accfile.

mwlist

list of arguments for markwear.accfile.

collapse.by

dataset aggregation level. See argument format from strptime for options and details below.

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 format from strptime for options.

FUN.list

a named list of functions. See collapse.fun.

keep.extreme

logical flag. If FALSE (default) extreme values will be replaced by NAs. See markpa.accfile.

keep.error

logical flag. If FALSE (default) data errors as identified by errorCts will be replaced by NAs.

...

arguments for dateSummary.

Value

A data frame containing the following variables
collapse.byaggregation factor
fileidfile identifier
...named columns according to arguments FUN and labels of palist

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 http://discovery.ucl.ac.uk/1361699

Examples

Run this code

data(gt1m_sample)

collapse.accfile(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)
collapse.by fileid mean.counts mean.steps sedentary  light moderate vigorous
1  2011-12-08   test      117.63       1.87    293.75 243.75    29.75     4.00
2  2011-12-09   test      157.83       3.09    349.75 143.25    33.50    24.50
3  2011-12-10   test       79.75       2.35    468.25 177.25    24.25     6.25
4  2011-12-11   test       57.96       2.01    355.50 126.00     8.50     3.25
5  2011-12-12   test       70.05       1.87    455.50 157.25    19.50     6.00
6  2011-12-13   test       72.99       2.01    475.50 181.50    15.25     8.00
7  2011-12-14   test       79.94       2.03    476.25 210.50    20.25     8.50
8  2011-12-15   test       232.5          2      0.00   0.50     0.00     0.00
9  2011-12-16   test         NaN        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
Warning message:
In collapse.accfile(gt1m_sample, palist = list(value = c(0, 100, 2000,  :
  NAs imputed where extreme counts found


collapse.accfile(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)
collapse.by fileid mean.counts sd.counts 95th.counts mean.steps sd.steps
1  2011-12-08   test      117.63    216.12       529.4       1.87     3.24
2  2011-12-09   test       201.1    567.65      1085.6       3.09     6.41
3  2011-12-10   test       81.97    221.33       465.5       2.35     5.88
4  2011-12-11   test        59.8    172.08      320.35       2.01     5.36
5  2011-12-12   test       70.05    188.49         401       1.87     4.91
6  2011-12-13   test       74.08    207.55      386.85       2.01     5.28
7  2011-12-14   test       87.42    275.27       415.3       2.03     5.57
8  2011-12-15   test       232.5    222.74      374.25          2     2.83
9  2011-12-16   test         NaN      <NA>        <NA>        NaN     <NA>
  95th.steps sedentary  light moderate vigorous extreme_values non-wear
1          8    293.75 243.75    29.75     4.00           0.00   388.75
2         20    349.75 143.25    33.50    24.50           6.00   883.00
3         15    468.25 177.25    24.25     6.25           0.50   763.50
4         12    355.50 126.00     8.50     3.25           0.25   946.50
5         11    455.50 157.25    19.50     6.00           0.00   801.75
6         12    475.50 181.50    15.25     8.00           0.25   759.50
7         11    476.25 210.50    20.25     8.50           1.50   723.00
8        3.8      0.00   0.50     0.00     0.00           0.00  1439.50
9       <NA>      0.00   0.00     0.00     0.00           0.00   187.50