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rename sib to denap in the variables names to avoid confusion #967
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@vincentvanhees
vincentvanhees committed Sep 2, 2024
1 parent 2763b9f commit bfab494
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Showing 4 changed files with 35 additions and 47 deletions.
38 changes: 13 additions & 25 deletions R/g.part5.analyseRest.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ g.part5.analyseRest = function(sibreport = NULL, dsummary = NULL,
} else {
dsummary[di,fi:(fi + 2)] = c(0, 0, 0)
}
ds_names[fi:(fi + 2)] = c(paste0("mdur_sib_overl_", name),
paste0("tdur_sib_overl_", name),
paste0("perc_sib_overl_", name))
ds_names[fi:(fi + 2)] = c(paste0("mdur_denap_overl_", name),
paste0("tdur_denap_overl_", name),
paste0("perc_denap_overl_", name))
fi = fi + 3
# Overlap selfreportwith sib
if (length(xi) > 0) {
Expand All @@ -40,9 +40,9 @@ g.part5.analyseRest = function(sibreport = NULL, dsummary = NULL,
} else {
dsummary[di,fi:(fi + 2)] = c(0, 0, 0)
}
ds_names[fi:(fi + 2)] = c(paste0("mdur_", name, "_overl_sib"),
paste0("tdur_", name, "_overl_sib"),
paste0("perc_", name ,"_overl_sib"))
ds_names[fi:(fi + 2)] = c(paste0("mdur_", name, "_overl_denap"),
paste0("tdur_", name, "_overl_denap"),
paste0("perc_", name ,"_overl_denap"))
fi = fi + 3
invisible(list(fi = fi, ds_names = ds_names, dsummary = dsummary, di = di))
}
Expand Down Expand Up @@ -223,26 +223,25 @@ g.part5.analyseRest = function(sibreport = NULL, dsummary = NULL,

# if (length(sleeplog_indices) > 1) browser()
# Count number of occurrences (do not count sleeplog because not informative)
dsummary[di,fi:(fi + 7)] = c(length(sibs_indices),
dsummary[di,fi:(fi + 6)] = c(length(sibs_indices),
length(nap_indices),
length(nonwear_indices),
length(SIBoverlapNap_indices),
length(SIBoverlapNonwear_indices),
length(NapOverlapSIB_indices),
length(NonwearOverlapSIB_indices),
length(SleeplogOverlapSIB_indices))
ds_names[fi:(fi + 7)] = c("nbouts_day_sib", "nbouts_day_srnap", "nbouts_day_srnonw",
"noverl_sib_srnap", "noverl_sib_srnonw",
"noverl_srnap_sib", "noverl_srnonw_sib", "noverl_srsleep_sib")
fi = fi + 8
length(NonwearOverlapSIB_indices))
ds_names[fi:(fi + 6)] = c("nbouts_day_denap", "nbouts_day_srnap", "nbouts_day_srnonw",
"noverl_denap_srnap", "noverl_denap_srnonw",
"noverl_srnap_denap", "noverl_srnonw_denap")
fi = fi + 7
# mean and total duration in sib per day
if (length(sibs_indices) > 0) {
dsummary[di,fi:(fi + 1)] = c(mean(srep_tmp$duration[sibs_indices]),
sum(srep_tmp$duration[sibs_indices]))
} else {
dsummary[di,fi:(fi + 1)] = c(0, 0)
}
ds_names[fi:(fi + 1)] = c("frag_mean_dur_sib_day", "dur_day_sib_min")
ds_names[fi:(fi + 1)] = c("frag_mean_dur_denap_day", "dur_day_denap_min")
fi = fi + 2
# mean and total duration in self-reported naps per day
if (length(nap_indices) > 0) {
Expand Down Expand Up @@ -288,17 +287,6 @@ g.part5.analyseRest = function(sibreport = NULL, dsummary = NULL,
sumobject = so
)
dsummary = so$dsummary; ds_names = so$ds_names; fi = so$fi
# Self-reported sleep (window could be time in bed, this depends on what user used in part 4)
so = summarise_overlap(
srep_tmp,
X = "SIBoverlapSleeplog",
Y = "SleeplogOverlapSIB",
xi = SIBoverlapSleeplog_indices,
yi = SleeplogOverlapSIB_indices,
name = "srsleep",
sumobject = so
)
dsummary = so$dsummary; ds_names = so$ds_names; fi = so$fi
rm(srep_tmp)
} else {
fi = fi + 33
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test_chainof5parts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,7 @@ test_that("chainof5parts", {
expect_true(dir.exists(dirname))
expect_true(file.exists(rn[1]))
expect_that(nrow(output),equals(5)) # changed because OO window is exported
expect_that(ncol(output),equals(205))
expect_that(ncol(output),equals(198))
expect_that(round(as.numeric(output$wakeup[2]), digits = 4), equals(36))
expect_that(as.numeric(output$dur_day_spt_min[4]), equals(1150)) # WW window duration
expect_that(as.numeric(output$dur_day_spt_min[5]), equals(1680)) # OO window duration
Expand Down
30 changes: 15 additions & 15 deletions tests/testthat/test_part5_analyseRest.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,12 +31,12 @@ test_that("Overlap 1 nap and 1 sib", {
names(dsummary) = ds_names
dsummary = as.data.frame(t(dsummary))

expect_equal(dsummary$nbouts_day_sib, 1)
expect_equal(dsummary$nbouts_day_denap, 1)
expect_equal(dsummary$nbouts_day_srnap, 1)
expect_equal(dsummary$frag_mean_dur_sib_day, 15)
expect_equal(dsummary$frag_mean_dur_denap_day, 15)
expect_equal(dsummary$frag_mean_dur_srnap_day, 20)
expect_equal(dsummary$perc_sib_overl_srnap, 100)
expect_equal(dsummary$perc_srnap_overl_sib, 75)
expect_equal(dsummary$perc_denap_overl_srnap, 100)
expect_equal(dsummary$perc_srnap_overl_denap, 75)
expect_equal(sum(dsummary), 323)
})

Expand All @@ -61,13 +61,13 @@ test_that("Overlap 1 nonwear and 1 sib", {
names(dsummary) = ds_names
dsummary = as.data.frame(t(dsummary))

expect_equal(dsummary$nbouts_day_sib, 1)
expect_equal(dsummary$nbouts_day_denap, 1)
expect_equal(dsummary$nbouts_day_srnonw, 1)
expect_equal(dsummary$frag_mean_dur_sib_day, 15)
expect_equal(dsummary$frag_mean_dur_denap_day, 15)
expect_equal(dsummary$frag_mean_dur_srnonw_day, 20)
expect_equal(dsummary$perc_sib_overl_srnonw, 100)
expect_equal(dsummary$perc_srnonw_overl_sib, 75)
expect_equal(sum(dsummary), 324)
expect_equal(dsummary$perc_denap_overl_srnonw, 100)
expect_equal(dsummary$perc_srnonw_overl_denap, 75)
expect_equal(sum(dsummary), 323)
})


Expand Down Expand Up @@ -95,17 +95,17 @@ test_that("No overlap 1 nonwear, 1 nap, and 1 sib", {
names(dsummary) = ds_names
dsummary = as.data.frame(t(dsummary))

expect_equal(ncol(dsummary), 34)
expect_equal(ncol(dsummary), 27)
expect_equal(nrow(dsummary), 1)
expect_equal(dsummary$nbouts_day_sib, 1)
expect_equal(dsummary$nbouts_day_denap, 1)
expect_equal(dsummary$nbouts_day_srnap, 1)
expect_equal(dsummary$nbouts_day_srnonw, 1)
expect_equal(dsummary$frag_mean_dur_sib_day, 20)
expect_equal(dsummary$frag_mean_dur_denap_day, 20)
expect_equal(dsummary$frag_mean_dur_srnap_day, 20)
expect_equal(dsummary$frag_mean_dur_srnonw_day, 20)
expect_equal(dsummary$perc_sib_overl_srnap, 0)
expect_equal(dsummary$perc_sib_overl_srnonw, 0)
expect_equal(dsummary$perc_srnonw_overl_sib, 0)
expect_equal(dsummary$perc_denap_overl_srnap, 0)
expect_equal(dsummary$perc_denap_overl_srnonw, 0)
expect_equal(dsummary$perc_srnonw_overl_denap, 0)
expect_equal(sum(dsummary, na.rm = TRUE), 129)

})
12 changes: 6 additions & 6 deletions vignettes/GGIRoutput.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -380,13 +380,13 @@ vigorous activity:
| nap_totalduration | Total nap duration, only calculated when argument do.sibreport = TRUE, currently optimised for 3.5-year old. See function documentation for function `g.part5.classifyNaps` in the [GGIR function documentation (pdf)](https:/CRAN.R-project.org/package=GGIR/GGIR.pdf). |
| sibreport_n_items | Only created if `do.sibreport = TRUE`. Number of items in the sibreport |
| sibreport_n_items_day | Only created if `do.sibreport = TRUE`. Number of items in the sibreport for this specific day |
| nbouts_day_X | Only created if `do.sibreport = TRUE`. Number of bouts in a day of X where X can be sib (sustained inactivity bout), srnap (self-reported nap) or srnonw (self-reported nonwear) |
| noverl_X | Only created if `do.sibreport = TRUE`. Number of overlapping bouts in a day of X where X can be sib_srnap, sib_srnonw, srnap_sib, or srnonw_sib |
| nbouts_X | Only created if `do.sibreport = TRUE`. Number of bouts in a day of X where X can be a detected nap (denap), srnap (self-reported nap) or srnonw (self-reported nonwear) |
| noverl_X | Only created if `do.sibreport = TRUE`. Number of overlapping bouts in a day of X where X can be denap_srnap, denap_srnonw, srnap_denap, or srnonw_denap |
| frag_mean_dur_X_day | Only created if `do.sibreport = TRUE`. Mean duration of X per day, where X can be sib, srnap or srnonw |
| dur_day_X_min | Only created if `do.sibreport = TRUE`. Total duration in minutes of X per day, where X can be sib, srnap or srnonw |
| mdur_X_overl_Y | Only created if `do.sibreport = TRUE`. Mean duration of the overlap between X and Y, which are combinations of sib, srnap or srnonw |
| tdur_X_overl_Y | Only created if `do.sibreport = TRUE`. Total duration in minutes of the overlap between X and Y, which are combinations of sib, srnap or srnonw |
| perc_X_overl_Y | Only created if `do.sibreport = TRUE`. Percentage of overlap between X and Y, which are combinations of sib, srnap or srnonw |
| dur_X_min | Only created if `do.sibreport = TRUE`. Total duration in minutes of X per day, where X can be detect nap (denap), srnap or srnonw |
| mdur_X_overl_Y | Only created if `do.sibreport = TRUE`. Mean duration of the overlap between X and Y, which are combinations of denap, srnap or srnonw |
| tdur_X_overl_Y | Only created if `do.sibreport = TRUE`. Total duration in minutes of the overlap between X and Y, which are combinations of denap, srnap or srnonw |
| perc_X_overl_Y | Only created if `do.sibreport = TRUE`. Percentage of overlap between X and Y, which are combinations of denap, srnap or srnonw |


**Special note if you are working on compositional data analysis:**
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