tests/testthat/test-spikeanalysis.R

In jefferis/gphys: Analyse Electrophysiology Data Acquired by 'Neuromatic' / 'Igor Pro'

context("spike analysis")

test_that("lifetime_sparseness",{
  spikes=CollectSpikesFromSweeps(
    system.file('igor','spikes','nm20110914c4',package='gphys'),
    subdir='BLOCKI',sweeps=0:4)
  od=OdourResponseFromSpikes(spikes, responseWindow =c(2200,2700),
                             baselineWindow = c(0,2000))
  expect_warning(S<-lifetime_sparseness(od), 'Zeroing 19 responses')
  expect_equal(S, c(1, 1, 1, 0.977589526376588, 0.96039603960396))
  
  # check what happens with NAs
  od2=od
  # -ve response -> NA
  od2[5,'cVA']=NA
  # +ve response -> NA
  od2[4,'IAA']=NA
  # nb difference in baseline for cell 4 is due to loss of a positive response
  expect_equal(lifetime_sparseness(od2),
               c(1, 1, 1, 0.979202772963605, 0.95049504950495))
  
  expect_warning(S3<-lifetime_sparseness(od2, minodours = 1.0),
                 'too few odours')
  expect_equal(S3, c(1, 1, 1, NA, NA))
})