Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fixes to issue259, 262, and metric ENMOa now better facilitated #264

Merged
merged 11 commits into from
Feb 28, 2020
Merged

Fixes to issue259, 262, and metric ENMOa now better facilitated #264

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
67975d1
fixes related to issue #259
vincentvanhees Feb 18, 2020
74fd426
remove before_install section to check whether it is still needed
vincentvanhees Feb 18, 2020
533534d
#259 g.part5 tidied up with more comments, and wake-detection for fir…
vincentvanhees Feb 26, 2020
8daf02e
edits to the code comments, no changes to the code itself
vincentvanhees Feb 26, 2020
eb1cbb2
added check that output object has size larger than zero, otherwise i…
vincentvanhees Feb 26, 2020
96f129b
added ENMOa to possible metrics for time spent in intensity level cal…
vincentvanhees Feb 27, 2020
f4db67e
minor edit to shorten line length
vincentvanhees Feb 27, 2020
a59707f
fixing typo
vincentvanhees Feb 27, 2020
32201fa
addresses #262 close #262
vincentvanhees Feb 28, 2020
c271bcd
explanation added to vignette on how to use published cut-points
vincentvanhees Feb 28, 2020
111a45a
fix merge conflicts
vincentvanhees Feb 28, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions R/g.analyse.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,7 @@ g.analyse = function(I,C,M,IMP,qlevels=c(),qwindow=c(0,24),quantiletype = 7,L5M
HFENplusi = which(colnames(metashort) == "HFENplus")
MADi = which(colnames(metashort) == "MAD")
ENi = which(colnames(metashort) == "EN")
ENMOai = which(colnames(metashort) == "ENMOa")
ANYANGLEi = which(colnames(M$metashort) %in% c("anglex","angley","anglez") == TRUE)
if (length(ANYANGLEi) == 0) ANYANGLEi = -1
if (length(ENMOi) == 0) ENMOi = -1
Expand All @@ -149,6 +150,7 @@ g.analyse = function(I,C,M,IMP,qlevels=c(),qwindow=c(0,24),quantiletype = 7,L5M
if (length(HFENplusi) == 0) HFENplusi = -1
if (length(MADi) == 0) MADi = -1
if (length(ENi) == 0) ENi = -1
if (length(ENMOai) == 0) ENMOai = -1
#===============================================
# Extract features from the imputed data
qcheck = r5long
Expand Down Expand Up @@ -176,14 +178,13 @@ g.analyse = function(I,C,M,IMP,qlevels=c(),qwindow=c(0,24),quantiletype = 7,L5M
qlevels_names = output_avday$qlevels_names
ML5AD=output_avday$ML5AD
ML5AD_names = output_avday$ML5AD_names

#--------------------------------------------------------------
# Analysis per day
if (doperday == TRUE) {
output_perday = g.analyse.perday(selectdaysfile, ndays, firstmidnighti, time, nfeatures,
window.summary.size, qwindow, midnightsi, metashort, averageday,
ENMOi, LFENMOi, BFENi, ENi,
HFENi, HFENplusi, MADi, doiglevels, nfulldays, lastmidnight,
HFENi, HFENplusi, MADi, ENMOai, doiglevels, nfulldays, lastmidnight,
ws3, ws2, qcheck, fname, idloc, BodyLocation, wdayname,
tooshort, includedaycrit, winhr,L5M5window, M5L5res,
doquan, qlevels, quantiletype, doilevels, ilevels, iglevels, domvpa,
Expand Down
4 changes: 2 additions & 2 deletions R/g.analyse.perday.R
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
g.analyse.perday = function(selectdaysfile, ndays, firstmidnighti, time, nfeatures,
window.summary.size, qwindow, midnightsi, metashort, averageday,
ENMOi, LFENMOi, BFENi, ENi, HFENi, HFENplusi, MADi,
ENMOi, LFENMOi, BFENi, ENi, HFENi, HFENplusi, MADi, ENMOai,
doiglevels, nfulldays,lastmidnight, ws3, ws2, qcheck,
fname, idloc, BodyLocation, wdayname, tooshort, includedaycrit,
winhr, L5M5window, M5L5res,
Expand Down Expand Up @@ -300,7 +300,7 @@ g.analyse.perday = function(selectdaysfile, ndays, firstmidnighti, time, nfeatur
}
# Starting filling output matrix daysummary with variables per day segment and full day.
if (mi == ENMOi | mi == LFENMOi | mi == BFENi |
mi == ENi | mi == HFENi | mi == HFENplusi | mi == MADi) {
mi == ENi | mi == HFENi | mi == HFENplusi | mi == MADi | mi == ENMOai) {
if (length(varnum) > ((60/ws3)*60*5.5)) { # Calculate values
exfi = 0
for (winhr_value in winhr) {
Expand Down
10 changes: 5 additions & 5 deletions R/g.part3.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
dir.create(file.path(paste(metadatadir,"/meta",sep=""),"sleep.qc"))
}
#------------------------------------------------------
fnames =dir(paste(metadatadir,"/meta/basic",sep=""))
fnames =dir(paste(metadatadir,"/meta/ms2.out",sep=""))
if (f1 > length(fnames) | f1 == 0) f1 = length(fnames)
if (f0 > length(fnames) | f0 == 0) f0 = 1
#========================================================================
Expand Down Expand Up @@ -67,14 +67,14 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
.export=functions2passon, .errorhandling=errhand) %myinfix% {
tryCatchResult = tryCatch({
# for (i in f0:f1) {
FI = file.info(paste(metadatadir,"/meta/basic/",fnames[i],sep=""))
FI = file.info(paste(metadatadir,"/meta/ms2.out/",fnames[i],sep=""))
if (is.na(FI$size) == TRUE) FI$size = 0
if (FI$size == 0 | is.na(FI$size) == TRUE | length(FI$size) == 0) {
cat(paste("P3 file ",fnames[i],sep=""))
cat("Filename not recognised")
}
fname = unlist(strsplit(fnames[i],".RData"))[1]
fname = unlist(strsplit(fname,"eta_"))[2]
# fname = unlist(strsplit(fname,"eta_"))[2]
#=========================================================
#check whether file has already been processed
#by comparing filename to read with list of processed files
Expand All @@ -92,8 +92,8 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
# Load previously stored meta-data from part1.R
cat(paste(" ",i,sep=""))
IMP = M = c()
load(paste(metadatadir,"/meta/basic/",fnames[i],sep=""))
load(paste(metadatadir,"/meta/ms2.out/",unlist(strsplit(fnames[i], "eta_"))[2],sep=""))
load(paste(metadatadir,"/meta/basic/meta_",fnames[i],sep=""))
load(paste(metadatadir,"/meta/ms2.out/",fnames[i],sep=""))
if (M$filecorrupt == FALSE & M$filetooshort == FALSE) {
# IMP = g.impute(M,I,strategy=1,hrs.del.start=0,hrs.del.end=0,maxdur=0)
SLE = g.sib.det(M,IMP,I,twd=c(-12,12),timethreshold=timethreshold,anglethreshold=anglethreshold,
Expand Down
15 changes: 12 additions & 3 deletions R/g.part4.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -421,6 +421,7 @@ g.part4 = function(datadir=c(),metadatadir=c(),f0=f0,f1=f1,idloc=1,loglocation =
calendardate[j] = DD$calendardate
}
spo = DD$spo
reversetime2 = reversetime3 = c()
if (daysleeper[j] == TRUE) {
if (loaddaysi == 1) {
w1 = which(spo[,3] >= 18) #only use periods ending after 6pm
Expand Down Expand Up @@ -461,14 +462,12 @@ g.part4 = function(datadir=c(),metadatadir=c(),f0=f0,f1=f1,idloc=1,loglocation =
name2 = paste("spo_day2",k,sep="")
tmpCmd = paste("spo = rbind(",name1,",",name2,")",sep="")
eval(parse(text=tmpCmd))
#reverse back the timestamps to remember that these timestamps were coming from different days
spo[which(spo[,3] >= 36),3] = spo[which(spo[,3] >= 36),3] - 24
spo[which(spo[,2] >= 36),2] = spo[which(spo[,2] >= 36),2] - 24
}
}
# spo is now a matrix of onset and wake for each sleep period (episode)
for (evi in 1:nrow(spo)) { #Now classify as being part of the SPT window or not
if (spo[evi,2] < SptWake & spo[evi,3] > SptOnset) { # = acconset < logwake & accwake > logonset

spo[evi,4] = 1 #nocturnal = all acc periods that end after diary onset and start before diary wake
# REDEFINITION OF ONSET/WAKE OF THIS PERIOD OVERLAPS
if (relyonsleeplog == TRUE) { #if TRUE then sleeplog value is assigned to accelerometer-based value for onset and wake up
Expand All @@ -481,6 +480,14 @@ g.part4 = function(datadir=c(),metadatadir=c(),f0=f0,f1=f1,idloc=1,loglocation =
}
}
}
if (daysleeper[j] == TRUE) {
# for the labelling above it was needed to have times > 36, but for the plotting
# time in the second day needs to be returned to a normal 24 hour scale.
reversetime2 = which(spo[,2] >= 36)
reversetime3 = which(spo[,3] >= 36)
if (length(reversetime2) > 0) spo[reversetime2,2] = spo[reversetime2,2] - 24
if (length(reversetime3) > 0) spo[reversetime3,3] = spo[reversetime3,3] - 24
}
#------------------------------------------------------------------------
# Variable 'spo' contains all the sleep periods FOR ONE SLEEP DEFINITION
# Variable 'spocum' contains all the sleep periods FOR MULTIPLE SLEEP DEFINITIONS
Expand Down Expand Up @@ -556,6 +563,8 @@ g.part4 = function(datadir=c(),metadatadir=c(),f0=f0,f1=f1,idloc=1,loglocation =

#------------------------------------
# ACCELEROMETER
if (is.matrix(spocum.t) == FALSE) spocum.t = as.matrix(spocum.t) # seems needed in rare occasions
if (ncol(spocum.t) < 4 & nrow(spocum.t) > 3) spocum.t = t(spocum.t) # seems needed in rare occasions
if (length(which(as.numeric(spocum.t[,4]) == 1)) > 0) {
rtl = which(spocum.t[,4] == 1)
nightsummary[sumi,3] =spocum.t[rtl[1],2]
Expand Down
Loading