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+version https://git-lfs.github.com/spec/v1 +oid sha256:999106c49d61372fe82e08d951637282ed2ce1be19a22ca76868d2313d0aefc6 +size 29057 diff --git a/paper/data/ggir_outputs/output_sub001/results/visualisation_sleep.pdf b/paper/data/ggir_outputs/output_sub001/results/visualisation_sleep.pdf new file mode 100644 index 0000000..7d23453 Binary files /dev/null and b/paper/data/ggir_outputs/output_sub001/results/visualisation_sleep.pdf differ diff --git a/paper/data/raw/sub001.gt3x b/paper/data/raw/sub001.gt3x new file mode 100644 index 0000000..473f1b3 --- /dev/null +++ b/paper/data/raw/sub001.gt3x @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6bef62e2d4f483a461e8f85ee95a4302d13e49c0f0d8fdda17ca3e24eb86ad6c +size 337136171 diff --git a/paper/data/scripts/run_ggir.R b/paper/data/scripts/run_ggir.R new file mode 100644 index 0000000..f4061c3 --- /dev/null +++ b/paper/data/scripts/run_ggir.R @@ -0,0 +1,97 @@ +############################################################################### +# +# Script to process actigraphy data from ActiGraph watches on GGIR +# +# Tested with GGIR version 3.2-6 +# +# Created by Nathalia Bianchini Esper +# May 2023 +# +############################################################################### + +library(GGIR) + + GGIR(#======================================= + # INPUT NEEDED: + mode=c(1,2,3,4,5), + datadir="/Users/nathalia.esper/Documents/Ongoing_Projects/Actigraphy/actisleep_paper/data/raw/sub001.gt3x", + outputdir="/Users/nathalia.esper/Documents/Ongoing_Projects/Actigraphy/actisleep_paper/data/outputs", + studyname="sub001", + f0=0, f1=0, + overwrite = TRUE, + idloc=6, + print.filename=TRUE, + storefolderstructure = FALSE, + dformat=2, + mon=3, + do.parallel=FALSE, + #------------------------------- + # Part 1: + #------------------------------- + desiredtz = "America/New_York", + do.enmo = TRUE, + do.anglez=TRUE, + do.hfen = FALSE, + windowsizes = c(5,900,3600), + do.cal=TRUE, + chunksize=1, + printsummary=TRUE, + #------------------------------- + # Part 2: + #------------------------------- + strategy = 1, + hrs.del.start = 0, + hrs.del.end = 0, + maxdur = 0, + winhr = c(5,10), + epochvalues2csv=TRUE, + L5M5window = c(0,24), + M5L5res = 10, + qlevels = c(c(1380/1440),c(1410/1440)), + qwindow=c(0,24), + ilevels = c(seq(0,400,by=50),8000), + mvpathreshold =c(125), + do.imp=TRUE, + #------------------------------- + # Part 3: + # (detection of sustained inactivity periods as needed for sleep detection in g.part4) + #------------------------------- + timethreshold= c(5), + anglethreshold = 5, + ignorenonwear = TRUE, + nonwear_approach = "2023", + #------------------------------- + # Part 4: + # （Labels detected sustained inactivity periods by g.part3 as either nocturnal sleep or daytime sustained inactivity) + #------------------------------- + excludefirstlast = FALSE, + includenightcrit = 12, + def.noc.sleep = c(1), + outliers.only = FALSE, + relyonguider = TRUE, + sleeplogidnum = TRUE, + do.visual = TRUE, + do.sibreport = TRUE, + criterror = 0, + #------------------------------- + # Part 5: + #------------------------------- + threshold.lig = c(30,40,50), + threshold.mod = c(100,120,125), + threshold.vig = c(400,500), + boutcriter = 0.8, + boutcriter.in = 0.9, + boutcriter.lig = 0.8, + boutcriter.mvpa = 0.8, + boutdur.in = c(10,20,30), + boutdur.lig = c(1,5, 10), + boutdur.mvpa = c(1,5,10), + timewindow = c("WW", "MM"), + # ----------------------------------- + # Report generation + # ----------------------------------- + do.report=c(2,4,5), + visualreport=TRUE, + dofirstpage = TRUE, + viewingwindow=2 +)