tests/testthat/test_recordingEndSleepHour.R

In wadpac/GGIR: Raw Accelerometer Data Analysis

library(GGIR)
context("recordingEndSleepHour")
test_that("recordingEndSleepHour works as expected", {
  skip_on_cran()
  #=======================
  create_test_acc_csv(Nmin = 3.5 * 1440) # ends at 20:45
  fn = "123A_testaccfile.csv"
  tz = "Europe/Amsterdam"
  # this should NOT trigger data expansion
  GGIR(mode = 1, datadir = fn, outputdir = getwd(), 
       studyname = "test", overwrite = TRUE, 
       recordingEndSleepHour = 21, desiredtz = tz,
       visualreport = FALSE, do.report = c(), verbose = FALSE)
  rn = dir("output_test/meta/basic/", full.names = TRUE)
  load(rn[1])
  expect_true(nrow(M$metashort) == 60300)
  # expect_true(M$metashort$timestamp[nrow(M$metashort)] == "2016-06-25T20:44:55+0200")
  
  # errors and warnings work properly
  expect_error( # error from using expand_tail_max_hour instead of new argument
    GGIR(mode = 1, datadir = fn, outputdir = getwd(), 
         studyname = "test", overwrite = TRUE,  desiredtz = tz,
         expand_tail_max_hours = 5, recordingEndSleepHour = NULL,
         visualreport = FALSE, do.report = c(), verbose = FALSE)
  )
  expect_warning( # warning from using both expand_tail_max_hour and recordingEndSleepHour
    GGIR(mode = 1, datadir = fn, outputdir = getwd(), 
         studyname = "test", overwrite = TRUE, desiredtz = tz,
         expand_tail_max_hours = 5, recordingEndSleepHour = 20,
         visualreport = FALSE, do.report = c(), verbose = FALSE)
  )
  
  expect_error( # error from recordingEndSleepHour being too early,
    # this should not produce any output
    GGIR(datadir = fn, outputdir = getwd(),
         studyname = "test", overwrite = TRUE, desiredtz = tz,
         recordingEndSleepHour = 6,
         minimum_MM_length.part5 = 15, verbose = FALSE)
  )
  
  
  # No warning, this should work
  GGIR(datadir = fn, outputdir = getwd(),
       studyname = "test", overwrite = TRUE, desiredtz = tz,
       recordingEndSleepHour = 20, do.anglex = TRUE, do.angley = TRUE,
       minimum_MM_length.part5 = 6, verbose = FALSE)
  rn = dir("output_test/meta/basic/", full.names = TRUE)
  load(rn[1])
  expect_true(nrow(M$metashort) > 60300) # metashort is expanded
  
  # expanded time is not reports
  p2 = read.csv("output_test/results/part2_daysummary.csv")
  expect_equal(p2$N.hours[nrow(p2)], 20.75)  # N hours in last day does not include the expanded time
  
  p4 = read.csv("output_test/results/part4_nightsummary_sleep_cleaned.csv")
  p4full = read.csv("output_test/results/QC/part4_nightsummary_sleep_full.csv")
  expect_equal(nrow(p4), 3) # Night 3 is not in the part 4 reports
  expect_equal(nrow(p4full), 3) # Night 3 is not in the part 4 reports
  expect_equal(sum(p4$sleeponset), 62.77)
  expect_equal(sum(p4$wakeup), 93.505)
  expect_equal(sum(p4$guider_onset), 62.775)
  expect_equal(sum(p4$guider_wakeup), 93.506)
  expect_equal(sum(p4$number_sib_sleepperiod), 114)
  expect_true(all(is.na(p4$longitudinal_axis)))
  
  p5 = read.csv("output_test/results/part5_daysummary_MM_L40M100V400_T5A5.csv")
  expect_equal(nrow(p5), 4) # expanded day appears in MM report
  expect_true(p5$dur_day_spt_min[nrow(p5)] < 23*60) # but expanded time is not accounted for in estimates
  
  #================================================================
  # Redo but now with sensor.location="hip", HASPT.algo = "HorAngle", and all three angles
  # we do not expect sleep to end in last hour here. Further, this allows for improving
  # coverage for the hip-attachment scenario for which we do not have specific unit
  # tests yet. By re-using the test file from this unit test we do not have to create it 
  # twice.

  # No warning, this should work
  GGIR(datadir = fn, outputdir = getwd(),
       studyname = "test", overwrite = TRUE, desiredtz = tz,
       recordingEndSleepHour = 20, do.anglex = TRUE, do.angley = TRUE,
       save_ms5rawlevels = TRUE, sensor.location = "hip", HASPT.algo = "HorAngle",
       save_ms5raw_format = "RData", sleepwindowType = "TimeInBed",
       minimum_MM_length.part5 = 6, verbose = FALSE)
  rn = dir("output_test/meta/basic/", full.names = TRUE)
  load(rn[1])
  expect_true(nrow(M$metashort) > 60300) # metashort is expanded
  
  # expanded time is not reports
  p2 = read.csv("output_test/results/part2_daysummary.csv")
  expect_equal(p2$N.hours[nrow(p2)], 20.75)  # N hours in last day does not include the expanded time
  
  p4 = read.csv("output_test/results/part4_nightsummary_sleep_cleaned.csv")
  p4full = read.csv("output_test/results/QC/part4_nightsummary_sleep_full.csv")
  expect_equal(nrow(p4), 3) # Night 3 is not in the part 4 reports
  expect_equal(nrow(p4full), 3) # Night 3 is not in the part 4 reports
  expect_equal(sum(p4$sleeponset), 62.1)
  expect_equal(sum(p4$wakeup), 81.096)
  expect_equal(sum(p4$guider_inbedStart), 53.17, tolerance = 0.005)
  expect_equal(sum(p4$guider_inbedEnd), 86.85, tolerance = 0.005)
  expect_equal(sum(p4$number_sib_sleepperiod), 24)
  expect_equal(sum(p4$sleepefficiency), 0.501)
  expect_equal(sum(p4$longitudinal_axis), 9)
  
  p5 = read.csv("output_test/results/part5_daysummary_MM_L40M100V400_T5A5.csv")
  expect_equal(nrow(p5), 3) # expanded day appears in MM report
  expect_true(p5$dur_day_spt_min[nrow(p5)] < 23*60) # but expanded time is not accounted for in estimates
  
  # test that time series output has all expected columns including the multiple angle columns
  # this does not align with the focus on sleep in this unit test, but if we have to 
  # write a separate unit test for it then the functions needs to be run twice.
  ts_file = "output_test/meta/ms5.outraw/40_100_400/123A_testaccfile_T5A5.RData"
  expect_true(file.exists(ts_file))
  load(ts_file)
  expect_true(all(c("timenum", "ACC", "SleepPeriodTime", "invalidepoch",
                    "guider", "window", "angle", "anglex", "angley",
                    "class_id", "invalid_fullwindow", "invalid_sleepperiod",
                    "invalid_wakinghours", "timestamp") %in% names(mdat)))
  
  #========================================================
  # Test require_complete_lastnight_part5 = TRUE
  create_test_acc_csv(Nmin = 3 * 1440) # ends at 8:45
  # delete config.csv such that GGIR uses its own default parameter values
  if (file.exists("output_test/config.csv"))  unlink("output_test/config.csv", recursive = TRUE)
  GGIR(datadir = fn, outputdir = getwd(), mode = 1:5,
       studyname = "test", overwrite = TRUE, desiredtz = tz, 
       verbose = FALSE, require_complete_lastnight_part5 = TRUE,
       do.report = 5)
  p5 = read.csv("output_test/results/part5_daysummary_MM_L40M100V400_T5A5.csv")
  expect_equal(nrow(p5), 2) # last window is ignored from because the night ends at 8:45
  
  
  if (file.exists("output_test"))  unlink("output_test", recursive = TRUE)
  if (file.exists(fn)) file.remove(fn)
})