Answers.Body: <p>This is a great current discussion in the field.</p>
  <p>There is an entire Frontiers special issue from last year dedicated to it.</p>
  <p><a href="https://www.frontiersin.org/research-topics/15888/before-after-control-impact-baci-studies-in-the-ocean" rel="nofollow noreferrer">https://www.frontiersin.org/research-topics/15888/before-after-control-impact-baci-studies-in-the-ocean</a></p>
  <p>Also, Astarte Brown will be presenting on the topic of BACI with a During component integrated into it at the AN 2022 conference this week. Her poster abstract from a previous ASA meeting is here: <a href="https://www.researchgate.net/publication/356362837_Frequency_changes_in_humpback_whale_Megaptera_novaeangliae_song_units_in_response_to_small_boat_noise_Astarte_Brown_Advised_by_Kerri_D_Seger" rel="nofollow noreferrer">https://www.researchgate.net/publication/356362837_Frequency_changes_in_humpback_whale_Megaptera_novaeangliae_song_units_in_response_to_small_boat_noise_Astarte_Brown_Advised_by_Kerri_D_Seger</a></p>
  <p>She ran about 30 t-tests for different combinations of whether low frequency, high frequency, and bandwidth of a few specific song units were significantly different During and After as compared to Before boat noise was detected at the hydrophone. But since the same humpback whale song units can be slightly different from one another she only used units that didn't have visibly different contours. If there was a contour change in the same unit (like Unit A1 because Unit A2), then that was considered a structural change - which is also an option to evaluate.</p>
  <p>Researchers in Colombia have found the ICI (intercall interval) between song units changed before vs after boat passes. They did not parse out the ICI between specific song units - any song units could have been valid for analysis. So check out the discussion for why an ICI change after a boat passes may not mean that the whale is singing a more lento or rapid song - the units themselves may have changed to a slower or faster paced theme. So combining song unit specific ICI's ver thematic changes that inherently have different ICIs would be a good next step for investigation.</p>
  <p><a href="https://www.researchgate.net/publication/350390231_Understanding_Effects_of_Whale-Watching_Vessel_Noise_on_Humpback_Whale_Song_in_the_North_Pacific_Coast_of_Colombia_With_Propagation_Models_of_Masking_and_Acoustic_Data_Observations" rel="nofollow noreferrer">https://www.researchgate.net/publication/350390231_Understanding_Effects_of_Whale-Watching_Vessel_Noise_on_Humpback_Whale_Song_in_the_North_Pacific_Coast_of_Colombia_With_Propagation_Models_of_Masking_and_Acoustic_Data_Observations</a></p>
  <p>Anecdotally speaking, interpreting the behavioral impetus for any statistically significant differences between Before and During/After was more difficult. How do we really get into the head of a whale? Animals with less complex repertoires are easier to interpret any BACI changes, in my opinion. It has been difficult to make a study design to tease apart whether the disturbance we think of as a disturbance (i.e. noise from a boat) is really what caused a timing shift or frequency shift in the animal. Really - there are other things in the ocean that could elicit a response and we wouldn't never know about them. I would say keep the measurements of the acoustic features of as simple and basic as possible. IF there are significant changes in any of them, THEN start combining what that feature means in the larger context of the repertoire.</p>
  <p>For example, Astarte Brown will show at AN2022 that sometimes song units had a bandwidth that</p>
  <ol>
  <li>shifted down in frequency (Why? Maybe to make that unit travel further because the point of the unit is to call to faraway whales)</li>
  <li>shifted up in frequency (Why? Maybe to make that unit go up and out of the boat noise since that unit may only be needed for short-range communication)</li>
  <li>broadened (Why? Maybe to cover more frequencies in hopes that some of them will transmit through / not get masked by the boat noise and at least some information will propagate.)</li>
  <li>narrowed (Why? Maybe to put all the energy into the most important information carrying part of the call so the important stuff is less likely to get masked by boat noise if the energy from the less important pieces of information are redirected into a narrower bandwidth. a.k.a. get rid of the fluff.)</li>
  </ol>
  <p>IMO, at this point of exploration in applying BACI to an underwater acoustical context, any new discovery and how well that methodology to discover it worked is a good step forward. Be very clear in the limitations of the methods so that interpretations of the results don't get out of hand.</p>
  
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Answers.Text: Hey Kerri, thanks for this response! Do you think the challenges with complex vocals such as song make them too challenging for these types of studies then?
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Answers.Text: Hi Liz. No, I don't think their challenge should be avoided, I think you just have to evaluate very clean and easy-to-measure features of the complex vocals instead of qualitative features. e.g. duration of the same unit in the same phrase and whether it changes. Not just "the song changed". HOW did the song change? In number of harmonics, from shorter units to longer units, from singing to not singing, from lower peak frequency to higher peak frequency in the same unit or in all units or in just one unit?
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Answers.Body: <p>I can attempt the BACI vs. BAG part of the question.</p>
  <p>With a single recorder, you won't really have the means to do a Before-After Gradient.  The idea behind a BAG is that you set up multiple data collection points in a transect away from your impact area.  In this paper by <a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.674594/full" rel="nofollow noreferrer">Elizabeth Methratta</a>, she breaks down the differences between BACI and BAG experimental designs. She highlights how useful a BAG design is for looking at fixed points of anthropogenic activity; windfarms, drilling platforms, etc. The design looks at the effects over the distance gradient away from the impact event, and typically analyzes those results using a linear model (lme), a generalized additive model (gam), or a generalized additive mixed-model (gamm).</p>
  <p>With a single recorder, you could potentially conduct a BACI, depending on what your anthropogenic event is.  You could take measurements before-during-after the impact event. That would be your BAI of the BACI. If the event is, say, a boat passing, you could take the same measurements the next day at the same time, just with no boat. That would be your BAC.  It would be easier if you had two sensors, but you can make it work.</p>
  <p>As for the second part of your question, I would think occurrence of calls would be a good metric, or even more simply, presence/absence. If you understand what your detection radius is, you could use the 'snapshot' method to set a time frame, say a minute, and determine if you detect your species within that timeframe, your 'snapshot'. If it is there, that snapshot is species positive. You can then count how many species positive minutes you have in an hour, and determine species occurrence from there.</p>
  <p><strong>Reference</strong></p>
  <p>Methratta, E. T. (2021). Distance-based sampling methods for assessing the ecological effects of offshore wind farms: Synthesis and application to fisheries resource studies. Frontiers in Marine Science, 1062.</p>
  
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Answers.Text: Thanks so much for this and appreciate the reference!
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Body: <p>I would like to develop a study to look for potential effects of anthropogenic activities on marine mammal species using data from a single hydrophone. I know this limits me in terms of the way I can evaluate a marine mammal's vocal response to anthropogenic noise, so am wondering what an appropriate analysis might be.</p>
  <p>First I'm wondering if someone can explain the difference between a Before-After-Control-Impact (BACI), a Beyond-BACI, and a Before-After-Gradient (BAG) design.</p>
  <p>Secondly, I know that looking at call amplitude might not be the best metric given the location of a calling animal is largely unknown (unless using propagation modeling to get at source level, which complicates things I think), and wondering what the best call parameter to look at might be (e.g. occurrence of calls, frequency specs as in <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121711" rel="noreferrer">Papale et al 2015</a>, etc.). Appreciate any thoughts/advice!</p>
  
Tags: <anthropogenic-noise><marine-mammals>
Title: Selecting an Accurate Before-During-After Analytical Framework
ThreadText: # Selecting an Accurate Before-During-After Analytical Framework
  
  (Asked by: username_0 on 2022-07-08)
  
  I would like to develop a study to look for potential effects of anthropogenic activities on marine mammal species using data from a single hydrophone. I know this limits me in terms of the way I can evaluate a marine mammal's vocal response to anthropogenic noise, so am wondering what an appropriate analysis might be.
  
  First I'm wondering if someone can explain the difference between a Before-After-Control-Impact (BACI), a Beyond-BACI, and a Before-After-Gradient (BAG) design.
  
  Secondly, I know that looking at call amplitude might not be the best metric given the location of a calling animal is largely unknown (unless using propagation modeling to get at source level, which complicates things I think), and wondering what the best call parameter to look at might be (e.g. occurrence of calls, frequency specs as in [Papale et al 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121711), etc.). Appreciate any thoughts/advice!
  
  **Tags:** anthropogenic-noise, marine-mammals
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2022-07-08. Score: 7 | Accepted answer
  
  I can attempt the BACI vs. BAG part of the question.
  
  With a single recorder, you won't really have the means to do a Before-After Gradient. The idea behind a BAG is that you set up multiple data collection points in a transect away from your impact area. In this paper by [Elizabeth Methratta](https://www.frontiersin.org/articles/10.3389/fmars.2021.674594/full), she breaks down the differences between BACI and BAG experimental designs. She highlights how useful a BAG design is for looking at fixed points of anthropogenic activity; windfarms, drilling platforms, etc. The design looks at the effects over the distance gradient away from the impact event, and typically analyzes those results using a linear model (lme), a generalized additive model (gam), or a generalized additive mixed-model (gamm).
  
  With a single recorder, you could potentially conduct a BACI, depending on what your anthropogenic event is. You could take measurements before-during-after the impact event. That would be your BAI of the BACI. If the event is, say, a boat passing, you could take the same measurements the next day at the same time, just with no boat. That would be your BAC. It would be easier if you had two sensors, but you can make it work.
  
  As for the second part of your question, I would think occurrence of calls would be a good metric, or even more simply, presence/absence. If you understand what your detection radius is, you could use the 'snapshot' method to set a time frame, say a minute, and determine if you detect your species within that timeframe, your 'snapshot'. If it is there, that snapshot is species positive. You can then count how many species positive minutes you have in an hour, and determine species occurrence from there.
  
  **Reference**
  
  Methratta, E. T. (2021). Distance-based sampling methods for assessing the ecological effects of offshore wind farms: Synthesis and application to fisheries resource studies. Frontiers in Marine Science, 1062.
  
  > **Comments:**
  > **username_0**: Thanks so much for this and appreciate the reference!  
  
  ---
  
  ### Answer by username_1 on 2022-07-08. Score: 4
  
  This is a great current discussion in the field.
  
  There is an entire Frontiers special issue from last year dedicated to it.
  
  <https://www.frontiersin.org/research-topics/15888/before-after-control-impact-baci-studies-in-the-ocean>
  
  Also, Astarte Brown will be presenting on the topic of BACI with a During component integrated into it at the AN 2022 conference this week. Her poster abstract from a previous ASA meeting is here: <https://www.researchgate.net/publication/356362837_Frequency_changes_in_humpback_whale_Megaptera_novaeangliae_song_units_in_response_to_small_boat_noise_Astarte_Brown_Advised_by_username_1_D_Seger>
  
  She ran about 30 t-tests for different combinations of whether low frequency, high frequency, and bandwidth of a few specific song units were significantly different During and After as compared to Before boat noise was detected at the hydrophone. But since the same humpback whale song units can be slightly different from one another she only used units that didn't have visibly different contours. If there was a contour change in the same unit (like Unit A1 because Unit A2), then that was considered a structural change - which is also an option to evaluate.
  
  Researchers in Colombia have found the ICI (intercall interval) between song units changed before vs after boat passes. They did not parse out the ICI between specific song units - any song units could have been valid for analysis. So check out the discussion for why an ICI change after a boat passes may not mean that the whale is singing a more lento or rapid song - the units themselves may have changed to a slower or faster paced theme. So combining song unit specific ICI's ver thematic changes that inherently have different ICIs would be a good next step for investigation.
  
  <https://www.researchgate.net/publication/350390231_Understanding_Effects_of_Whale-Watching_Vessel_Noise_on_Humpback_Whale_Song_in_the_North_Pacific_Coast_of_Colombia_With_Propagation_Models_of_Masking_and_Acoustic_Data_Observations>
  
  Anecdotally speaking, interpreting the behavioral impetus for any statistically significant differences between Before and During/After was more difficult. How do we really get into the head of a whale? Animals with less complex repertoires are easier to interpret any BACI changes, in my opinion. It has been difficult to make a study design to tease apart whether the disturbance we think of as a disturbance (i.e. noise from a boat) is really what caused a timing shift or frequency shift in the animal. Really - there are other things in the ocean that could elicit a response and we wouldn't never know about them. I would say keep the measurements of the acoustic features of as simple and basic as possible. IF there are significant changes in any of them, THEN start combining what that feature means in the larger context of the repertoire.
  
  For example, Astarte Brown will show at AN2022 that sometimes song units had a bandwidth that
  
  1. shifted down in frequency (Why? Maybe to make that unit travel further because the point of the unit is to call to faraway whales)
  2. shifted up in frequency (Why? Maybe to make that unit go up and out of the boat noise since that unit may only be needed for short-range communication)
  3. broadened (Why? Maybe to cover more frequencies in hopes that some of them will transmit through / not get masked by the boat noise and at least some information will propagate.)
  4. narrowed (Why? Maybe to put all the energy into the most important information carrying part of the call so the important stuff is less likely to get masked by boat noise if the energy from the less important pieces of information are redirected into a narrower bandwidth. a.k.a. get rid of the fluff.)
  
  IMO, at this point of exploration in applying BACI to an underwater acoustical context, any new discovery and how well that methodology to discover it worked is a good step forward. Be very clear in the limitations of the methods so that interpretations of the results don't get out of hand.
  
  > **Comments:**
  > **username_0**: Hey username_1, thanks for this response! Do you think the challenges with complex vocals such as song make them too challenging for these types of studies then?  
  > **username_1**: Hi Liz. No, I don't think their challenge should be avoided, I think you just have to evaluate very clean and easy-to-measure features of the complex vocals instead of qualitative features. e.g. duration of the same unit in the same phrase and whether it changes. Not just "the song changed". HOW did the song change? In number of harmonics, from shorter units to longer units, from singing to not singing, from lower peak frequency to higher peak frequency in the same unit or in all units or in just one unit?  
  
  ---
  
  