README: Characterising underwater noise and changes in harbour porpoise behaviour during the decommissioning of an oil and gas platform

https://doi.org/10.5061/dryad.xwdbrv1kh

Data packages associated with the paper “Characterising underwater noise and changes in harbour porpoise behaviour during the decommissioning of an oil and gas platform” (DOI: 10.1016/j.marpolbul.2024.116083). This data package includes the datasets and R code required to repeat all the analyses of the paper.

Description of the data and file structure

The data package consists of the following 9 data files:

1. Filename: OFB_MMSDecommissioning_CPODexe_Clickdetails.csv
2. Filename: OFB_MMSDecommissioning_CPODexe_HP-PPM_perHOUR.txt
3. Filename: OFB_MMSDecommissioning_CPODexe_ClickCounts.txt
4. Filename: OFB_MMSDecommissioning_HP-PPM-BPM_perHOUR.csv
5. Filename: OFB_MMSDecommissioning_CPODLocations.csv
6. Filename: OFB_MMSDecommissioning_DPH-BPH_Filtered_3minH-100000.csv
7. Filename: OFB_MMSDecommissioning_SPL-Loc294.csv
8. Filename: OFB_MMSDecommissioning_JackyLog_Report.csv
9. Filename: OFB_MMSDecommissioning_SPL30min_ActivityLog_Loc294_28-08-21to11-09-21.csv

1. Filename: OFB_MMSDecommissioning_CPODexe_Clickdetails.csv

Harbour porpoise echolocation click details between July and September 2021 extracted from CPODs using cpod.exe v. 2.044.

Twelve columns: Date, Minute, microsec, cycles, SPL_Pa, kHz, Bandwidth, end_kHz, Qn, TrN, location.id, depl

• Date is the date and time when the echolocation click was detected (YYYY-mm-dd HH:MM:SS, in UTC)
• Minute is the number of minutes since the start of 1900 at which the echolocation click was detected.
• Microsec is the microsecond in the minute when the echolocation click was detected.
• Cycles is the duration of the echolocation click represented as the number of cycles at the dominant frequency.
• SPL_Pa is the value of the maximum sound pressure level of the echolocation click in Pascals.
• kHz is the dominant frequency of the echolocation click based on zero-crossing intervals.
• Bandwidth is a measure on an arbitrary scale of frequency bandwidth (zero bandwidth sounds are pure tones; high bandwidth sounds resemble white noise, cracking, crunching and other such sounds that have no easily recognisable pitch).
• end_kHz is the frequency value derived from the last zero crossing interval.
• Qn is the numeric assessment of the cpod.exe Kerno echolocation click classifier (High: 3, Moderate: 2 and Low quality: 1).
• TrN is the numeric identifier of the echolocation click train.
• Location.id is the numeric identifier of the location at which that CPOD was deployed.
• Depl is the numeric identifier of the CPOD deployment

2. Filename: OFB_MMSDecommissioning_CPODexe_HP-PPM_perHOUR.txt

Data from cpod.exe summarising harbour porpoise detections per hour between the 28th August and the 11th September 2021.

Seven columns: depl, location.id, date, datetimehour, ppm, por.pres, total.minutes.

• Depl is the numeric identifier of the CPOD deployment.
• Location.id is the numeric identifier of the location at which that CPOD was deployed.
• Date is the date (YYYY-mm-dd).
• Datetimehour is the date and time (YYYY-mm-dd HH:MM:SS, in UTC).
• Ppm is the Porpoise Positive minutes (PPM), the number of minutes per hour during which harbour porpoises’ echolocation clicks were detected (0-60).
• Por.pres is the presence/absence of harbour porpoises’ detections during that hour (1: present; 0: absent).
• Total.minutes is the total number of minutes that the CPOD was working during that hour.

3. Filename: OFB_MMSDecommissioning_CPODexe_ClickCounts.txt

Data from cpod.exe summarising information on CPOD scan limit and maximum number of recorded clicks detected by CPODs between the 28th August and the 11th September 2021.

Eight columns: File, ChunkEnd, Nfiltered, Nall, MinsOn, depl, location.id, clicklimit.

• File is the CPOD filename.
• ChunkEnd is the date and time (dd/mm/YYYY HH:MM, in UTC).
• Nfiltered is the number of echolocation clicks classified as porpoise clicks by the KERNO classifier (High and moderate quality) detected in that minute.
• Nall is the total number of echolocation clicks detected in that minute.
• MinsOn indicates whether the CPOD was working during that minute (1: yes, 0: no)
• Depl is the numeric identifier of the CPOD deployment.
• Location.id is the numeric identifier of the location at which that CPOD was deployed.
• Clicklimit is the maximum number of clicks per minute the CPOD was set to record (scan limit).

4. Filename: OFB_MMSDecommissioning_HP-PPM-BPM_perHOUR.csv

Dataset that combines cpod.exe summary files and echolocation buzzes per hour detected by CPODs between the 28th August and the 11th September 2021.

Nine columns: depl, location.id, date, datetimehour, ppm, por.pres, bpm, buzz.pres, total.minutes.

• Depl is the numeric identifier of the CPOD deployment.
• Location.id is the numeric identifier of the location at which that CPOD was deployed.
• Date is the date (YYYY-mm-dd).
• Datetimehour is the date and time (YYYY-mm-dd HH:MM:SS, in UTC).
• Ppm is the total number of minutes per hour when porpoise echolocation clicks were detected (Porpoise Positive Minutes).
• Por.pres is the presence/absence of harbour porpoises’ detections during that hour (1: present; 0: absent).
• Bpm is the total number of minutes per hour when echolocation buzzes were detected (Buzz Positive Minutes).
• Buzz.pres is the presence/absence of harbour porpoises' echolocation buzzes detections during that hour (1: present; 0: absent).
• Total.minutes is the number of minutes that the CPOD was working during that hour.

5. Filename: OFB_MMSDecommissioning_CPODLocations.csv

Dataset that includes the locations of all CPOD deployments.

Four columns: depl, location.id, latitude, longitude.

• Depl is the numeric identifier of the POD deployment.
• Location.id is the numeric identifier of the location at which the CPOD was deployed.
• Latitude is the latitude (decimal degrees).
• Longitude is the longitude (decimal degrees).
• Depth is the depth (m) of the location at which the CPOD was deployed.
• Jacky.dist.m is the distance to the Jacky O&G platform (in m; Jacky Wellhead: Latitude 58.18395, Longitude -2.9799).
• Beabra.dist.m is the distance to the Beatrice Bravo O&G platform (in m; Beatrice Bravo: Latitude 58.14721, Longitude -3.02155).

6. Filename: OFB_MMSDecommissioning_DPH-BPH_Filtered_3minH-100000.csv

Dataset that combines hourly porpoise detections Before/During/After decommissioning to assess variation in harbour porpoise occurrence and foraging activity.

Ten columns: depl, location.id, date, jacky.period, jacky.dist.m, beabra.dist.m, closest.structure, tot.hours, dph, bph.

• Depl is the numeric identifier of the CPOD deployment.
• Location.id is the numeric identifier of the location at which the POD was deployed.
• Date is the date (YYYY-mm-dd).
• Jacky.period indicates the decommissioning period: Before (28th August to 1st September), During (2nd to 6th September) and After (7th to 11th September).
• Jacky.dist.m is the distance to the Jacky O&G platform (in m; Jacky Wellhead: Latitude 58.18395, Longitude -2.9799).
• Beabra.dist.m is the distance to the Beatrice Bravo O&G platform (in m; Beatrice Bravo: Latitude 58.14721, Longitude -3.02155).
• Closest.structure indicates the closest offshore structure to the CPOD. NA when distance to any structure is > 200 m.
• Tot.hours is the number of hours that the CPOD was working during that day.
• Dph is the number of harbour porpoise detection positive hours (DPH) during that day.
• Bph is the total number of hours per day when echolocation buzzes were detected (Buzz Positive Hours).

7. Filename: OFB_MMSDecommissioning_SPL-Loc294.csv

Broadband sound pressure levels in 30-minute bins extracted from the Soundtrap (ST600HF, Ocean Instruments) deployed at location 294 (Latitude 58.178, Longitude -2.986) between the 28th August and the 11th September 2021.

Three columns: location.id, datetime, SPL.

• Location.id is the numeric identifier of the location at which the SoundTrap was deployed.
• Datetime is the date and time (YYYY-mm-dd HH:MM:SS, in UTC).
• SPL is the total broadband sound pressure levels (dB re 1 µPa). Broadband SPL values in 30-minute bins were calculated using the sum of the square pressure magnitude values from a FFT of the signal across the whole frequency range (from 100 Hz to 48 kHz).

8. Filename: OFB_MMSDecommissioning_JackyLog_Report.csv

Decommissioning activity log as provided by the developer.

Four columns: notes, activity.start, activity.end, details.

• Notes indicates the location of the activity.
• Activity.start is the date and time when the decommissioning activity started (dd/mm/YYYY HH:MM, in UTC).
• Activity.end is the date and time when the decommissioning activity ended (dd/mm/YYYY HH:MM, in UTC).
• Details is the detailed information about the decommissioning activity.

9. Filename: OFB_MMSDecommissioning_SPL30min_ActivityLog_Loc294_28-08-21to11-09-21.csv

Dataset that combines broadband sound pressure levels and information on decommissioning activities in 30-minute bins.

Seven columns: location.id, date, datetime, SPL, jacky.period, thialf.present, Code.

• Location.id is the numeric identifier of the location at which the SoundTrap was deployed.
• Date is the date (YYYY-mm-dd).
• Datetime is the date and time (YYYY-mm-dd HH:MM:SS, in UTC).
• SPL is the total broadband sound pressure levels (dB re 1 µPa). Broadband SPL values in 30-minute bins were calculated using the sum of the square pressure magnitude values from a FFT of the signal across the whole frequency range (from 100 Hz to 48 kHz).
• Jacky.period indicates the decommissioning period: Before (28th August to 1st September), During (2nd to 6th September) and After (7th to 11th September).
• Thialf.present indicates the presence/absence of the Thialf crane vessel (1: present; 0: absent).
• Code indicates the decommissioning activity conducted (Cutting/Drilling/ROV test dive/Other). NA when there was no specified activity in the developer's activity log.

Sharing/Access information

NA

Code/Software

R code required to repeat all the analyses of the paper “Characterising underwater noise and changes in harbour porpoise behaviour during the decommissioning of an oil and gas platform”. Data processing and analyses were conducted in R (R Core Team, 2022) version 4.2.2.

R Code consists of 5 scripts:

1. Filename: OFB_MMSDecommissioning - 10km CPODs - Buzz extraction and summarise perHour.R
2. Filename: OFB_MMSDecommissioning - 10km CPODs - Create DPH and BPH perDay - Final dataset.R
3. Filename: OFB_MMSDecommissioning - 10km CPODs - Statistical Analyses.R
4. Filename: OFB_MMSDecommissioning - Noise - Dataset preparation.R
5. Filename: OFB_MMSDecommissioning - Noise - Statistical Analyses.R

1. Filename: OFB_MMSDecommissioning - 10km CPODs - Buzz extraction and summarise perHour.R

R code to extract buzzes from echolocation clicks and summarise them per hour.
R code requires input data files 1 and 2 (OFB_MMSDecommissioning_CPODexe_Clickdetails.csv and OFB_MMSDecommissioning_CPODexe_HP-PPM_perHOUR.txt) and produces data file 4 (OFB_MMSDecommissioning_HP-PPM-BPM_perHOUR.csv).

2. Filename: OFB_MMSDecommissioning - 10km CPODs - Create DPH and BPH perDay - Final dataset.R

R code to create the dataset required to assess changes in harbour porpoise behaviour before/during/after the decommissioning.
This code combines CPOD data and information on decommissioning activities.
R code requires input data files 3, 4 and 5 (OFB_MMSDecommissioning_CPODexe_ClickCounts.txt, OFB_MMSDecommissioning_HP-PPM-BPM_perHOUR.csv and OFB_MMSDecommissioning_CPODLocations.csv) and produces data file 6, the final CPOD dataset (OFB_MMSDecommissioning_DPH-BPH_Filtered_3minH-100000.csv).

3. Filename: OFB_MMSDecommissioning - 10km CPODs - Statistical Analyses.R

R code to perform the statistical analyses and assess the occurrence and foraging activity of harbour porpoises before/during/after decommissioning.
R code requires input data file 6 (OFB_MMSDecommissioning_DPH-BPH_Filtered_3minH-100000.csv).

4. Filename: OFB_MMSDecommissioning - Noise - Dataset preparation.R

R code to create the dataset required to characterise variation in underwater noise during decommissioning activities.
R code requires input data files 7 and 8 (OFB_MMSDecommissioning_SPL-Loc294.csv and OFB_MMSDecommissioning_JackyLog_Report.csv) and produces data file 9 (OFB_MMSDecommissioning_SPL30min_ActivityLog_Loc294_28-08-21to11-09-21.csv).

5. Filename: OFB_MMSDecommissioning - Noise - Statistical Analyses.R

R code to perform the statistical analyses and characterise variation in underwater noise during decommissioning activities.
R code requires input data file 9 (OFB_MMSDecommissioning_SPL30min_ActivityLog_Loc294_28-08-21to11-09-21.csv).