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Check for overlap in behaviors #7

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matiasandina opened this issue Oct 31, 2022 · 1 comment
Open

Check for overlap in behaviors #7

matiasandina opened this issue Oct 31, 2022 · 1 comment
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enhancement New feature or request

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@matiasandina
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As of today, StatEtho does not check for overlaps in behavior.
Should different behaviors be allowed to happen at the same time?
It's difficult to know beforehand if overlap is the result of a bug or ggethos working properly.
If the plot is large, it's difficult to visually inspect for overlap.
@matiasandina matiasandina added the enhancement New feature or request label Oct 31, 2022
@matiasandina
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matiasandina commented Apr 6, 2023 •
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This issue is somewhat difficult to solve if providing data where behavior doesn't change between continuous trials. Note that the overlap needs not be in the original data, it can be generated by our grouping of continuous runs. For example, animal was doing behavior "A" at the end of the trail and continued doing behavior "A" at the start of the next one. Our current approach will join those runs because they are continuous, unless being told not to. To give a particular example of this issue failing in daily usage:

library(tidyverse)
library(ggethos)
toy_df <- structure(list(trial_n = c(11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
                                     11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 
                                     12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 
                                     13, 13, 13, 13, 13, 13, 13, 13, 13), time = c(3632, 3634, 3636, 
                                                                                   3638, 3640, 3642, 3644, 3646, 3648, 3650, 3652, 3654, 3656, 3658, 
                                                                                   3660, 3662, 3664, 3666, 3668, 3670, 3672, 3674, 3676, 3678, 3680, 
                                                                                   3682, 3684, 3686, 3688, 3690, 3692, 3694, 3696, 3698, 3700, 3702, 
                                                                                   3704, 3706, 3708, 3710, 3712, 3714, 3716, 3718, 3720, 3722, 3724, 
                                                                                   3726, 3728, 3730, 3732, 3734, 3736, 3738, 3740, 3742, 3744, 3746, 
                                                                                   3748, 3750, 3752, 3754, 3756, 3758, 3760, 3762, 3764, 3766, 3768, 
                                                                                   3770, 3772, 3774, 3776, 3778, 3780, 3782, 3784, 3786, 3788, 3790, 
                                                                                   3792, 3794, 3796, 3798, 3800, 3802, 3804, 3806, 3808, 3810, 3812, 
                                                                                   3814, 3816, 3818, 3820, 3822, 3824, 3826, 3828, 3830, 3832, 3834, 
                                                                                   3836, 3838, 3840, 3842, 3844, 3846, 3848, 3850, 3852, 3854, 3856, 
                                                                                   3858, 3860, 3862, 3864, 3866, 3868, 3870, 3872, 3874, 3876, 3878, 
                                                                                   3880, 3882, 3884, 3886, 3888, 3890, 3892, 3894, 3896, 3898, 3900, 
                                                                                   3902, 3904, 3906, 3908, 3910, 3912, 3914, 3916, 3918, 3920, 3922, 
                                                                                   3924, 3926, 3928, 3930, 4486, 4488, 4490, 4492, 4494, 4496, 4498, 
                                                                                   4500, 4502, 4504, 4506, 4508, 4510, 4512, 4514, 4516, 4518, 4520, 
                                                                                   4522, 4524, 4526, 4528, 4530, 4532, 4534, 4536, 4538, 4540, 4542, 
                                                                                   4544, 4546, 4548, 4550, 4552, 4554, 4556, 4558, 4560, 4562, 4564, 
                                                                                   4566, 4568, 4570, 4572, 4574, 4576, 4578, 4580, 4582, 4584, 4586, 
                                                                                   4588, 4590, 4592, 4594, 4596, 4598, 4600, 4602, 4604, 4606, 4608, 
                                                                                   4610, 4612, 4614, 4616, 4618, 4620, 4622, 4624, 4626, 4628, 4630, 
                                                                                   4632, 4634, 4636, 4638, 4640, 4642, 4644, 4646, 4648, 4650, 4652, 
                                                                                   4654, 4656, 4658, 4660, 4662, 4664, 4666, 4668, 4670, 4672, 4674, 
                                                                                   4676, 4678, 4680, 4682, 4684, 4686, 4688, 4690, 4692, 4694, 4696, 
                                                                                   4698, 4700, 4702, 4704, 4706, 4708, 4710, 4712, 4714, 4716, 4718, 
                                                                                   4720, 4722, 4724, 4726, 4728, 4730, 4732, 4734, 4736, 4738, 4740, 
                                                                                   4742, 4744, 4746, 4748, 4750, 4752, 4754, 4756, 4758, 4760, 4762, 
                                                                                   4764, 4766, 4768, 4770, 4772, 4774, 4776, 4778, 4780, 4782, 4784, 
                                                                                   5364, 5366, 5368, 5370, 5372, 5374, 5376, 5378, 5380, 5382, 5384, 
                                                                                   5386, 5388, 5390, 5392, 5394, 5396, 5398, 5400, 5402, 5404, 5406, 
                                                                                   5408, 5410, 5412, 5414, 5416, 5418, 5420, 5422, 5424, 5426, 5428, 
                                                                                   5430, 5432, 5434, 5436, 5438, 5440, 5442, 5444, 5446, 5448, 5450, 
                                                                                   5452, 5454, 5456, 5458, 5460, 5462, 5464, 5466, 5468, 5470, 5472, 
                                                                                   5474, 5476, 5478, 5480, 5482, 5484, 5486, 5488, 5490, 5492, 5494, 
                                                                                   5496, 5498, 5500, 5502, 5504, 5506, 5508, 5510, 5512, 5514, 5516, 
                                                                                   5518, 5520, 5522, 5524, 5526, 5528, 5530, 5532, 5534, 5536, 5538, 
                                                                                   5540, 5542, 5544, 5546, 5548, 5550, 5552, 5554, 5556, 5558, 5560, 
                                                                                   5562, 5564, 5566, 5568, 5570, 5572, 5574, 5576, 5578, 5580, 5582, 
                                                                                   5584, 5586, 5588, 5590, 5592, 5594, 5596, 5598, 5600, 5602, 5604, 
                                                                                   5606, 5608, 5610, 5612, 5614, 5616, 5618, 5620, 5622, 5624, 5626, 
                                                                                   5628, 5630, 5632, 5634, 5636, 5638, 5640, 5642, 5644, 5646, 5648, 
                                                                                   5650, 5652, 5654, 5656, 5658, 5660, 5662), behavior = c("Wake", 
                                                                                                                                           "Wake", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Wake", "Wake", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Wake", 
                                                                                                                                           "Wake", "Wake", "Sleep", "Sleep", "Sleep", "Sleep", "Wake", "Wake", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", "Sleep", 
                                                                                                                                           "Sleep", "Sleep", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", "Wake", 
                                                                                                                                           "Wake", "Wake", "Wake")), row.names = c(NA, -450L), class = c("tbl_df", 
                                                                                                                                                                                                         "tbl", "data.frame"))

toy_df %>% 
  ggplot(aes(time, y=trial_n, behaviour = behavior, color=behavior)) + 
  geom_ethogram()
#> No observation interval provided, using guessed interval 2
#> Warning: Returning more (or less) than 1 row per `summarise()` group was deprecated in
#> dplyr 1.1.0.
#> ℹ Please use `reframe()` instead.
#> ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()`
#>   always returns an ungrouped data frame and adjust accordingly.
#> ℹ The deprecated feature was likely used in the ggethos package.
#>   Please report the issue to the authors.

I'm not showing the behavior with align_trials = T, but it also gets messed up because of the overlap.

This could be fixed by using group inside the ggplot call, which is awesome, and that's why we love ggplot2 so much. In a perfect world, I guess we could check for overlap at the exit of the ethogram calculation and throw a warning, suggesting to use group by whatever y was used

toy_df %>% 
  ggplot(aes(time, y=trial_n, behaviour = behavior, color=behavior, group=trial_n)) + 
  geom_ethogram()
#> No observation interval provided, using guessed interval 2

Another option, using get_ethogram() from #15, which also produces the same as above (not shown in the reprex).

toy_df %>% 
  group_by(trial_n) %>% 
  get_ethogram(time, behaviour = behavior) %>% 
  ggplot(aes(x = x, xend=xend, y=trial_n, yend=trial_n, color = behaviour)) +
  geom_segment(linewidth = 5)
#> Error in get_ethogram(., time, behaviour = behavior): could not find function "get_ethogram"

Created on 2023-04-06 with reprex v2.0.2

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@matiasandina