Skip to content

Commit

Permalink
Merge branch 'master' into azteca
Browse files Browse the repository at this point in the history
  • Loading branch information
@vincentvanhees
vincentvanhees committed Nov 22, 2024
2 parents 641e7a1 + 2cc32ce commit 6fc169a
Show file tree
Hide file tree
Showing 5 changed files with 54 additions and 59 deletions.
2 changes: 2 additions & 0 deletions NEWS.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@ this is consistent with functionality in the past. #1223

- Part 2: Add parameters nonwearFiltermaxHours and nonwearFilterWindow to give use the option to filter short lasting nighttime nonwear #1218.

- Part 5: Improved handling of partially available and non-available qwindow segments in the recording #1229

# CHANGES IN GGIR VERSION 3.1-6

- Part 6:
Expand Down
10 changes: 8 additions & 2 deletions R/g.fragmentation.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,14 @@ g.fragmentation = function(frag.metrics = c("mean", "TP", "Gini", "power",
} else {
do.frag = FALSE
}
# define expected output to standardize length and output names
if ("TP" %in% frag.metrics) {
output[["TP_IN2PA"]] = output[["TP_PA2IN"]] = output[["Nfrag_IN2PA"]] = output[["Nfrag_PA2IN"]] = NA
output[["TP_IN2LIPA"]] = output[["Nfrag_IN2LIPA"]] = NA
output[["TP_IN2MVPA"]] = output[["Nfrag_IN2MVPA"]] = NA
output[["Nfrag_LIPA"]] = output[["mean_dur_LIPA"]] = NA
output[["Nfrag_MVPA"]] = output[["mean_dur_MVPA"]] = NA
}
if (Nepochs > 1 & mode == "day") { # metrics that require more than just binary
#====================================================
# Convert LEVELS in three classes: Inactivity (1), Light = LIPA (2), and MVPA (3)
Expand Down Expand Up @@ -144,7 +152,6 @@ g.fragmentation = function(frag.metrics = c("mean", "TP", "Gini", "power",
}
#====================================================
# Binary fragmentation for the metrics that do not depend on multiple classes

if (mode == "day") {
x = rep(0,Nepochs)
is.na(x[is.na(LEVELS)]) = TRUE
Expand All @@ -155,7 +162,6 @@ g.fragmentation = function(frag.metrics = c("mean", "TP", "Gini", "power",
out = TransProb(x, a = 1, b = 0) #IN <-> PA
output[["Nfrag_PA"]] = out$Nba
output[["Nfrag_IN"]] = out$Nab

# Define default values
if ("mean" %in% frag.metrics) {
output[["mean_dur_PA"]] = output[["mean_dur_IN"]] = 0
Expand Down
5 changes: 3 additions & 2 deletions R/g.part5.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -537,9 +537,10 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
}
if (timewindowi == "MM" & si > 1) { # because first segment is always full window
if (("segment" %in% colnames(ts)) == FALSE) ts$segment = NA
ts$segment[segStart:segEnd] = si
if (!is.na(segStart) && !is.na(segEnd)) {
ts$segment[segStart:segEnd] = si
}
}

# Already store basic information about the file
# in the output matrix:
dsummary[si,fi:(fi + 1)] = c(ID, fnames.ms3[i])
Expand Down
72 changes: 26 additions & 46 deletions R/g.part5.definedays.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
qqq_backup = qqq
# in MM, also define segments of the day based on qwindow
if (!is.na(qqq[1]) & !is.na(qqq[2])) {
segments_timing = NULL
if (qqq[2] > Nts) qqq[2] = Nts
fullQqq = qqq[1]:qqq[2]
firstepoch = format(ts$time[qqq[1]], "%H:%M:%S")
Expand All @@ -74,55 +75,34 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
if (qwindow[1] != 0) qwindow = c(0, qwindow)
if (qwindow[length(qwindow)] != 24) qwindow = c(qwindow, 24)
}
# define segments timing in H:M:S format
breaks = qwindow2timestamp(qwindow, epochSize)
if (24 %in% qwindow) {
# 24:00:00: probably does not exist, replace by last timestamp in a day
# here, we consider N epochs per day plus 1 hour just in case we are deriving this in
# a 25-hour daylight saving time day
NepochPerDayPlusOneHr = ((25*3600) / epochSize)
latest_time_in_day = max(format(ts$time[1:pmin(Nts, NepochPerDayPlusOneHr)], format = "%H:%M:%S"))
breaks = gsub(pattern = "24:00:00", replacement = latest_time_in_day, x = breaks)
}
breaks_i = c()
for (bi in 1:length(breaks)) {
if (any(grepl(breaks[bi], ts$time[fullQqq]))) {
breaks_i[bi] = fullQqq[grep(breaks[bi], ts$time[fullQqq])][1]
} else {
breaks_i[bi] = qqq[1]
}
}
# build up segments
segments = list(qqq)
segments_timing = paste(firstepoch, lastepoch, sep = "-")
segments_names = "MM"
si = 2
do.segments = TRUE
if (length(qwindow) == 2) {
if (all((qwindow) == c(0, 24))) {
do.segments = FALSE
}
}
if (do.segments == TRUE) {
for (bi in 1:(length(breaks) - 1)) {
minusOne = ifelse(breaks[bi + 1] == lastepoch, 0, 1)
if (minusOne == 1) {
segments[[si]] = c(breaks_i[bi], breaks_i[bi + 1] - 1)
endOfSegment = subtractEpochFromTimeName(breaks[bi + 1], epochSize)
} else {
segments[[si]] = c(breaks_i[bi], breaks_i[bi + 1])
endOfSegment = breaks[bi + 1]
}
if (segments[[si]][2] < segments[[si]][1]) segments[[si]][2] = segments[[si]][1]
segments_timing[si] = paste(breaks[bi], endOfSegment, sep = "-")
if (is.null(qnames)) {
segments_names[si] = paste0("segment", bi)
} else {
segments_names[si] = paste(qnames[si - 1], qnames[si], sep = "-")
}
si = si + 1
}
startOfSegments = breaks[-length(breaks)]
endOfSegments = subtractEpochFromTimeName(breaks[-1], epochSize)
if (length(startOfSegments) > 1) { # when qwindow segments are defined, add fullwindow at the beginning
startOfSegments = c(firstepoch, startOfSegments)
endOfSegments = c(lastepoch, endOfSegments)
}
segments_timing = paste(startOfSegments, endOfSegments, sep = "-")
# define segment names based on qnames or segmentX
if (is.null(qnames)) {
segments_names = paste0("segment", 0:(length(segments_timing) - 1))
segments_names = gsub("segment0", "MM", segments_names)
} else {
segments_names = c("MM", paste(qnames[-length(qnames)], qnames[-1], sep = "-"))
}
# Get indices in ts for segments start and end limits
hms = format(ts$time[fullQqq], format = "%H:%M:%S")
segments = vector("list", length = length(segments_timing))
names(segments) = segments_timing
for (si in 1:length(segments_timing)) {
s0s1 = unlist(strsplit(segments_timing[si], split = "[-]"))
s0s1 = format(s0s1, format = "%H:%M:%S")
# tryCatch is needed in the case that the segment is not available in ts,
# then a no non-missing values warning would be triggered by the which function
segments[[si]] = tryCatch(range(fullQqq[which(hms >= s0s1[1] & hms <= s0s1[2])]), #segStart and segEnd
warning = function(w) rep(NA, 2))
}
}
} else if (timewindowi == "WW" || timewindowi == "OO") {
windowEdge = ifelse(timewindowi == "WW", yes = -1, no = 1)
Expand Down
24 changes: 15 additions & 9 deletions R/g.part5_analyseSegment.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,8 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,

#==========================
# The following is to avoid issue with merging sleep variables from part 4
# This code extract them the time series (ts) object created in g.part5
# Note that this means that for MM windows there can be multiple or no wake or onsets
date = as.Date(ts$time[segStart + 1], tz = params_general[["desiredtz"]])
# Note that this means that for MM windows there can be multiple or no wake or onsets in window
date = as.Date(ts$time[qqq[1]], tz = params_general[["desiredtz"]]) # changed segStart for qqq[1] in case segment is not available in this day
if (add_one_day_to_next_date == TRUE & timewindowi %in% c("WW", "OO")) { # see below for explanation
date = date + 1
add_one_day_to_next_date = FALSE
Expand Down Expand Up @@ -115,7 +114,10 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
sumSleep$acc_available[dayofinterest])
ds_names[fi:(fi + 5)] = c("night_number", "daysleeper", "cleaningcode",
"guider", "sleeplog_used", "acc_available"); fi = fi + 6
ts$guider[segStart:segEnd] = sumSleep$guider[dayofinterest] # add guider also to timeseries
if (!is.na(segStart) & !is.na(segEnd)) {
# segment available in time series
ts$guider[segStart:segEnd] = sumSleep$guider[dayofinterest] # add guider also to timeseries
}
} else {
dsummary[si,fi:(fi + 5)] = rep(NA, 6)
ds_names[fi:(fi + 5)] = c("night_number",
Expand All @@ -129,17 +131,21 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
# which differs between MM and WW
# Also, it allows for the analysis of the first day for those studies
# in which the accelerometer is started during the morning and the first day is of interest.
# qqq1 is the start of the day
# qqq2 is the end of the day
# qqq1 is the start of the day/segment
# qqq2 is the end of the day/segment
qqq1 = segStart
qqq2 = segEnd
# keep track of threshold value
dsummary[si, fi:(fi + 2)] = c(TRLi, TRMi, TRVi)
ds_names[fi:(fi + 2)] = c("TRLi", "TRMi", "TRVi")
fi = fi + 3
wlih = ((qqq2 - qqq1) + 1)/((60/ws3new) * 60)
if (qqq1 > length(LEVELS)) qqq1 = length(LEVELS)
sse = qqq1:qqq2
if (!is.na(qqq1)) {
if (qqq1 > length(LEVELS)) qqq1 = length(LEVELS)
sse = qqq1:qqq2
} else {
sse = NULL
}
doNext = FALSE
if (length(sse) >= 1) { #next
#============================================================
Expand Down Expand Up @@ -453,4 +459,4 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
doNext = doNext,
add_one_day_to_next_date = add_one_day_to_next_date
))
}
}

0 comments on commit 6fc169a

Please sign in to comment.