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set daysleep_offset default value #399

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merged 9 commits into from
Feb 26, 2021
Merged

set daysleep_offset default value #399

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685c707
set daysleep_offset default value
l-k- Feb 18, 2021
292e34a
minor cleanup
l-k- Feb 25, 2021
eb4ee15
report errors and warning for non-parallel execution in parts 1,2,3 a…
l-k- Feb 25, 2021
8d7c3c9
adding test to catch "object 'daysleep_offset' not found" error
l-k- Feb 25, 2021
53c024e
c() is NULL, which cannot be put into a vector; NA can be.
l-k- Feb 26, 2021
0a5701e
treat NA the same way you would a blank
l-k- Feb 26, 2021
2598a31
always use curly braces around multi-statement 'if' block
l-k- Feb 26, 2021
8eb3202
update docs to reflect change of IVIS_epochsize_seconds default value
l-k- Feb 26, 2021
83081a4
adding contributor name
l-k- Feb 26, 2021
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c() is NULL, which cannot be put into a vector; NA can be. 
c() is equivalent to NULL, which is causing problems in the following line in `g.analyse.perfile.R`:

filesummary[vi:(vi+3)] = c(InterdailyStability, IntradailyVariability,
                               IVIS_windowsize_minutes, IVIS_epochsize_seconds)

The thing is, NULL is not allowed in a vector, and so it's getting ignored, and we end up with a vector size of 3 instead of 4. This causes a warning when Part2 is run:

"number of items to replace is not a multiple of replacement length"

NA doesn't have this problem and can be used to represent a missing value.
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@l-k-
l-k- committed Feb 26, 2021
commit 53c024e4949d92e93eaaa84b57d1f5b97aab2fcc
4 changes: 2 additions & 2 deletions R/g.IVIS.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
g.IVIS = function(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds=c(), IVIS_windowsize_minutes = 60, IVIS.activity.metric = 1) {
if (!is.null(IVIS_epochsize_seconds)) {
g.IVIS = function(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds=NA, IVIS_windowsize_minutes = 60, IVIS.activity.metric = 1) {
if (!is.na(IVIS_epochsize_seconds)) {
warning("Argument IVIS_epochsize_seconds has been depricated")
}
IVIS_epochsize_seconds = IVIS_windowsize_minutes*60
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2 changes: 1 addition & 1 deletion R/g.part2.R
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Expand Up @@ -6,7 +6,7 @@ g.part2 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy = 1, hrs.d
boutcriter = 0.8,ndayswindow=7,idloc=1,do.imp=TRUE,storefolderstructure = FALSE,
overwrite=FALSE,epochvalues2csv=FALSE,mvpadur=c(1,5,10),selectdaysfile=c(),
window.summary.size=10,dayborder=0,bout.metric=2,closedbout=FALSE,desiredtz="",
IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = c(), iglevels = c(),
IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = NA, iglevels = c(),
IVIS.activity.metric=2, TimeSegments2ZeroFile=c(), qM5L5 = c(), do.parallel = TRUE,
myfun=c(), MX.ig.min.dur=10) {
snloc= 1
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2 changes: 1 addition & 1 deletion R/g.shell.GGIR.R
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Expand Up @@ -206,7 +206,7 @@ g.shell.GGIR = function(mode=1:5,datadir=c(),outputdir=c(),studyname=c(),f0=1,f1
if (exists("ndayswindow") == FALSE) ndayswindow = 7
if (exists("do.imp") == FALSE) do.imp = TRUE
if (exists("IVIS_windowsize_minutes") == FALSE) IVIS_windowsize_minutes=60
if (exists("IVIS_epochsize_seconds") == FALSE) IVIS_epochsize_seconds=c()
if (exists("IVIS_epochsize_seconds") == FALSE) IVIS_epochsize_seconds=NA
if (exists("mvpadur") == FALSE) mvpadur = c(1,5,10) # related to part 2 (functionality to anticipate part 5)
if (length(mvpadur) != 3) {
mvpadur = c(1,5,10)
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1 change: 0 additions & 1 deletion tests/testthat/test_part3_1_night.R
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Expand Up @@ -10,7 +10,6 @@ test_that("Part 3 identifies 1-night scenario", {
dn = "output_test"
if (file.exists(dn)) unlink(dn,recursive=TRUE)


# g.part# modules report errors and warnings only by printing them out to the console,
# so these are not true errors and warnings that would get caught by the testing module.
# Instead, grab the console output and parse out any errors we should know about.
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