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moving bout detection code to seperate function #653
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| detectEventBouts = function(myfun, varnum_event, varnum, | ||
| UnitReScale, daysummary, ds_names, | ||
| di, fi, ws3, boutnameEnding) { | ||
| if ("ebout.dur" %in% names(myfun) == FALSE) myfun$ebout.dur = c(1, 5, 10) | ||
| if ("ebout.th.cad" %in% names(myfun) == FALSE) myfun$ebout.th.cad = 30 | ||
| if ("ebout.th.acc" %in% names(myfun) == FALSE) myfun$ebout.th.acc = 50 | ||
| if ("ebout.criter" %in% names(myfun) == FALSE) myfun$ebout.criter = 0.8 | ||
| if ("ebout.condition" %in% names(myfun) == FALSE) myfun$ebout.condition = "AND" | ||
|
|
||
| # varnum = metashort[anwindices, mi] | ||
| cadence = varnum_event * (60/ws3) | ||
| # Event bouts | ||
| for (boutdur in myfun$ebout.dur) { | ||
| boutduration = boutdur * (60/ws3) # per minute | ||
| rr1 = matrix(0, length(varnum), 1) | ||
| if (myfun$ebout.condition == "AND") { | ||
| p = which(varnum * UnitReScale >= myfun$ebout.th.acc & | ||
| cadence >= myfun$ebout.th.cad); rr1[p] = 1 | ||
| } else if (myfun$ebout.condition == "OR") { | ||
| p = which(varnum * UnitReScale >= myfun$ebout.th.acc | | ||
| cadence >= myfun$ebout.th.cad); rr1[p] = 1 | ||
| } | ||
| getboutout = g.getbout(x = rr1, boutduration = boutduration, | ||
| boutcriter = myfun$ebout.criter, | ||
| bout.metric = 6, ws3 = ws3) | ||
| # time spent in bouts in minutes | ||
| eventbout = length(which(getboutout$x == 1)) / (60/ws3) | ||
| eboutname = paste0("ExtFunEvent_Bout_totdur_E", ws3, "S_B", boutdur, | ||
| "M", (myfun$ebout.criter * 100), | ||
| "%_cadT",myfun$ebout.th.cad,"_", | ||
| myfun$ebout.condition, | ||
| "_accT", myfun$ebout.th.acc) | ||
| ebout_varname = paste0(eboutname, "_", boutnameEnding) | ||
| # fi = correct_fi(di, ds_names, fi, varname = ebout_varname) | ||
| daysummary[di,fi] = eventbout # total time in ebouts | ||
| ds_names[fi] = ebout_varname; | ||
| fi = fi + 1 | ||
| # number of bouts | ||
| rle_bout = rle(as.numeric(getboutout$x)) | ||
| rle_bout1 = which(rle_bout$values == 1) | ||
| number_of_bouts = length(rle_bout1) | ||
|
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||
| eboutname = paste0("ExtFunEvent_Bout_number_E", ws3, "S_B", boutdur, | ||
| "M", (myfun$ebout.criter * 100), | ||
| "%_cadT",myfun$ebout.th.cad,"_", | ||
| myfun$ebout.condition, | ||
| "_accT", myfun$ebout.th.acc) | ||
| ebout_varname = paste0(eboutname, "_", boutnameEnding) | ||
| daysummary[di,fi] = number_of_bouts | ||
| ds_names[fi] = ebout_varname; | ||
| fi = fi + 1 | ||
| # average bout duration in minutes | ||
| if (number_of_bouts > 0) { | ||
| mn_dur_bouts = mean(rle_bout$lengths[which(rle_bout$values == 1)]) / (60/ws3) | ||
| } else { | ||
| mn_dur_bouts = 0 | ||
| } | ||
| eboutname = paste0("ExtFunEvent_Bout_meandur_E", ws3, "S_B", boutdur, | ||
| "M", (myfun$ebout.criter * 100), | ||
| "%_cadT",myfun$ebout.th.cad,"_", | ||
| myfun$ebout.condition, | ||
| "_accT", myfun$ebout.th.acc) | ||
| ebout_varname = paste0(eboutname, "_", boutnameEnding) | ||
| daysummary[di,fi] = mn_dur_bouts | ||
| ds_names[fi] = ebout_varname; | ||
| fi = fi + 1 | ||
| } | ||
| invisible(list(daysummary = daysummary, ds_names = ds_names, | ||
| fi = fi, di = di)) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| library(GGIR) | ||
| context("detectEventBouts") | ||
| test_that("Detect bouts in events", { | ||
| skip_on_cran() | ||
|
|
||
| # create dummy test data | ||
| metashort = data.frame(ENMO = c(rep(0, 24), rep(0.12, 36), rep(0, 24)), | ||
| step_count = c(rep(0, 24), rep(5, 36), rep(0, 24))) | ||
| cn_metashort = colnames(metashort) | ||
| anwindices = 1:84 | ||
| anwi_index = 1 | ||
| varnum = metashort$step_count[anwindices] | ||
| varnum_event = rep(0, length(varnum)) | ||
| varnum_event[which(metashort$ENMO[anwindices] > 0.05)] = 10 | ||
| ws3 = 5 | ||
| anwi_nameindices = "_1234hrs" | ||
| daysummary = matrix("", 1, 25) | ||
| fi = 1 | ||
| di = 1 | ||
| ds_names = "" | ||
| myfun = list(ilevels = c(0, 50, 100), | ||
| clevels = c(0, 30, 50), | ||
| qlevels = c(0.25, 0.5, 0.75), | ||
| ebout.dur = c(1, 5, 10), | ||
| ebout.th.cad = 30, | ||
| ebout.th.acc = 50, | ||
| ebout.criter = 1, | ||
| ebout.condition = "AND") | ||
|
|
||
| # run function | ||
| eventBouts = detectEventBouts(myfun, varnum_event = varnum_event, | ||
| varnum = varnum, | ||
| UnitReScale = 1000, | ||
| daysummary = daysummary, | ||
| ds_names = ds_names, | ||
| di = di, fi = fi, | ||
| ws3 = ws3, | ||
| boutnameEnding = "_anyRandomText") | ||
|
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||
| expect_equal(eventBouts$daysummary[1], "3") | ||
| expect_equal(eventBouts$daysummary[2], "1") | ||
| expect_equal(eventBouts$daysummary[3], "3") | ||
| expect_equal(eventBouts$daysummary[4], "0") | ||
| expect_equal(eventBouts$daysummary[5], "0") | ||
| expect_equal(eventBouts$ds_names[5], "ExtFunEvent_Bout_number_E5S_B5M100%_cadT30_AND_accT50__anyRandomText") | ||
|
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||
| }) |