README

# Title of Dataset:"Variation in soundscapes and harbour porpoise occurrence prior to pile-driving at two offshore windfarms"
---
Passive Acoustic Monitoring data collection was funded by the Marine Mammal Monitoring Programmes
for the construction of the Beatrice and Moray East offshore windfarms.
Contact for queries is Aude Benhemma-Le Gall, aude.benhemma-legall@abdn.ac.uk
Automated Identification System vessel-tracking raw data are not shared in this repository, as the University of Aberdeen has signed a Data Licence Agreement.
However, summaries of these vessel data are provided as txt file.

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## R scripts
Name - Description
### 1_Benhemma-Le_Gall_Allocate_HRP_to_piling_timeline.R
Based on the piling timeline of both the Beatrice and Moray East offshore windfarms, we identifed piling bouts of at least 12 hours,
filtered the subset of turbine locations where piling bouts had at least a three-day gap between the end of piling at the previous turbine location
and the start of piling at the focal turbine location and allocated Hours Relative to Piling (HRP) from 48 hours prior to the start of Acoustic Deterence Devices
(ADD) and piling activity.
### 2_Benhemma-Le_Gall_Estimate_piling_vessel_arrival_time_at_construction_site.R
Using the piling vessel Daily Progress Reports and the hammer log reports, we estimated when the piling vessel anchored or jacked-up at the construction site.
These preliminary analyses helped us decide to focus the main analyses on the period 48 hours prior to the start of piling at each location.
We identified the locations at which the piling vessel arrived on site > 48 hours before the start of piling activities. These locations will not be included in
the main analyses.
### 3_Benhemma-Le_Gall_Modelling_HRP_vs_vessel_intensity_and_porpoise_occurrence.R
Variation in harbour porpoise occurrence and vessel intensity per hours relative to piling at a subset of piling locations are being investigated for both
offshore windfarms.
### 4_Benhemma-Le_Gall_Construction_activities_per_HRP.R
The proportion of activities conducted by the piling vessel was estimated and visualised per hours relative to piling for a subset of piling locations.
Variation in vessel intensity per activities is investigated and reported in the supplementary material.
### 5_Benhemma-Le_Gall_Noise_data_modelling.R
Broadband noise levels recorded continuously over two weeks at each offshore windfarm site were analysed for a subset of three piling locations, from 24 hours prior to
the start of piling. The minimum distance of any vessels and the mean distance from the piling vessel were included in the model when comparing the differences in
broadband noise levels between the two windfarms.
## Description of the Data and file structure
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## DATA INPUT
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### Benhemma-Le_Gall_MMMP_Piling summary by 12 hour piling bout up to 27Feb20.txt

* bout_no: Piling bout ID
* turbine: Wind turbine ID
* pile: Pile ID (i.e. FORE, MP, AFT)
* sttime: start of piling (dd/mm/yyyy hh:mm, in GMT)
* endtime: end of piling (dd/mm/yyyy hh:mm, in GMT)
* sttime.ADD: start of Acoustic Deterrent Device (ADD) use (dd/mm/yyyy hh:mm, in GMT)
* endtime.ADD: end of ADD use (dd/mm/yyyy hh:mm, in GMT)

### Benhemma-Le_Gall_MMMP_Piling summary by piling bout with ADD activation_2Feb18.txt

* turbine: Wind turbine ID
* pile_no: Pile ID (i.e. A1, A2, B1, B2)
* bout_no: Piling bout ID
* start_time: start of piling (dd/mm/yyyy hh:mm, in GMT)
* end_time: end of piling (dd/mm/yyyy hh:mm, in GMT)
* ADD_st: start of ADD use (dd/mm/yyyy hh:mm, in GMT)
* ADD_end: end of ADD use (dd/mm/yyyy hh:mm, in GMT)

### Benhemma-Le_Gall_MMMP_SHL Yudin DPR Data Record_20180415_corrected.txt

* Date: Date of the Beatrice piling vessel activity (dd/mm/yyyy)
* Start time: Start time of activity (hh:mm, in BST)
* End time: End time of activity (hh:mm, in BST)
* SHL Task Code: Seaway Heavy Lifting (SHL; independent offshore installation contractor) Task code
* Duration: Activity duration (hh:mm)
* BOWL Code: Beatrice Offshore Windfarm Limited (BOWL) activity code
* Location: Piling vessel location

### Benhemma-Le_Gall_MMMP_Apollo activities May19-February20.txt

* Activity Group: Moray East piling vessel activity group ID
* Activity: Piling vessel actitivity
* Location: Piling vessel location
* Start: Start time of activity (hh:mm, in BST)
* Finish: End time of activity (hh:mm, in BST)
* Duration: Activity duration (hh:mm)
* Date: Date of the piling vessel activity (dd/mm/yyyy)
* sttime: Start date and time of activity (dd/mm/yyyy hh:mm, in BST)
* endtime: End date and time of activity (dd/mm/yyyy hh:mm, in BST)

### Benhemma-Le_Gall_MMMP_Before_hours_relative_to_piling_2017-19-20.txt

* Posix: Date and time of CPOD data logger (dd/mm/yyyy hh:mm, in GMT)
* Porp.min: Number of harbour porpoise clicks logged per minute
* Nall: Number of clicks logged in one minute
* MinsOn: Number of minute logging data by CPOD
* Location.ID: CPOD site ID
* Deployment.no: CPOD deployment number
* turbine: Wind turbine ID
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* bout_12hr: Piling bout ID per piling campaign
* piling_BA: Presence/abscense of ADD and piling activity
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* julday: Julian day ID
* year: Year
* month: Month of the year
* hour: Hour of the day [1;24]
* DPM: Harbour porpoise Detection Positive Minute (DPM): Presence/abscense of harbour porpoise clicks per minute

### Benhemma-Le_Gall_MMMP_Distance_between_CPOD_OWT.txt

* Depl_loc: CPOD deployment number and site ID
* turbine_ID: Wind turbine ID at which piling occurred
* distance.km: distance between the CPOD deployment site and the turbine/piling location (in km)

### Benhemma-Le_Gall_MMMP_PAM_2017_5km_buffer_48HRP_Before_without_yudin.txt
### Benhemma-Le_Gall_MMMP_PAM_2019-20_5km_buffer_48HRP_Before_without_apollo.txt

* Deployment.number: CPOD deployment number
* Location.ID: CPOD site ID
* bout_12hr: Piling bout ID per piling campaign
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* n_boat: Number of AIS-vessels within a 5 km buffer around the CPOD site per hour relative to piling
* n_AIS_dot: Number of 5-min interpolated AIS dots within a 5 km buffer around the CPOD site per hour relative to piling
* duration_min: Cumulative vessel duration (min) within a 5 km buffer area around CPOD site per hour relative to piling
* min_dist: Minimum distance (per HRP) between CPOD site and AIS vessels passing within a 5 km buffer area around that CPOD site
* mean_dist: Mean distance (per HRP) between CPOD site and AIS vessels passing within a 5 km buffer area around that CPOD site
* boat_density: Number of individual AIS-vessels per kilometer squared per hour relative to piling
* boat_intensity: Sum of residence times for all AIS-vessels per kilometer squared per hour relative to piling

### Benhemma-Le_Gall_MMMP_POD_Deployments_PAM_Database_20200708.txt

* Deployment number: CPOD deployment number
* Deployment type: Project related to the deployment (i.e. Marine Mammal Monitoring Programme)
* POD number: CPOD unique ID
* Deployment date: CPOD deployment date (dd/mm/yyyy)
* Deployment time GMT: CPOD deployment time (hh:mm:ss)
* Location ID: CPOD site ID
* Latitude: Latitude (in Decimal Degrees, WGS84)
* Longitude: Longitude (in Decimal Degrees, WGS84)
* Depth: Site depth (m)
* Data end date: CPOD data end date (dd/mm/yyyy)
* Data end time GMT: CPOD data end time (hh:mm:ss)

### Benhemma-Le_Gall_MMMP_Distance_yudin_to_short-term_noise_recorder_dpl_2017.txt

* NAME: Piling vessel name (Stanislav Yudin)
* Posix: Date and time of the piling vessel interpolated location (dd/mm/yyyy hh:mm)
* lat: Latitude (in Decimal Degrees, WGS84)
* lon: Longitude (in Decimal Degrees, WGS84)
* 903_201: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 903 and site ID: 201)
* 905_202: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 905 and site ID: 202)
* 907_203: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 907 and site ID: 203)

### Benhemma-Le_Gall_MMMP_Distance_apollo_to_short-term_noise_recorder_dpl_2019.txt

* Name: Piling vessel name (Apollo)
* Posix: Date and time of the piling vessel interpolated location (dd/mm/yyyy hh:mm)
* lat: Latitude (in Decimal Degrees, WGS84)
* lon: Longitude (in Decimal Degrees, WGS84)
* 1055_247: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 1055 and site ID: 247)
* 1056_248: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 1056 and site ID: 248)
* 1057_249: Distance between the piling vessel and one of the noise recorders (in km) (deployment ID: 1057 and site ID: 249)

### Benhemma-Le_Gall_MMMP_ST_2017-19_5km_buffer_48HRP_Before.txt

* Deployment.no: SoundTrap deployment number
* Location: SoundTrap site ID
* bout_12hr: Piling bout ID per piling campaign
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* n_boat: Number of AIS-vessels within a 5 km buffer around the SoundTrap site per hour relative to piling
* n_AIS_dot: Number of 5-min interpolated AIS dots within a 5 km buffer around the SoundTrap site per hour relative to piling
* duration_min: Cumulative vessel duration (min) within a 5 km buffer area around SoundTrap site per hour relative to piling
* min_dist: Minimum distance (per HRP) between SoundTrap site and AIS vessels passing within a 5 km buffer area around that SoundTrap site
* mean_dist: Mean distance (per HRP) between SoundTrap site and AIS vessels passing within a 5 km buffer area around that SoundTrap site
* boat_density: Number of individual AIS-vessels per kilometer squared per hour relative to piling
* boat_intensity: Sum of residence times for all AIS-vessels per kilometer squared per hour relative to piling
* PV_n_AIS_dot: Number of the piling vessel interpolated AIS dots within a 5 km buffer around the SoundTrap site per hour relative to piling
* PV_duration_min: Cumulative duration (min) of the piling vessel within a 5 km buffer area around SoundTrap site per hour relative to piling
* PV_min_dist: Minimum distance (per HRP) between SoundTrap site and the piling vessel passing within a 5 km buffer area around that SoundTrap site
* PV_mean_dist: Mean distance (per HRP) between SoundTrap site and the piling vessel passing within a 5 km buffer area around that SoundTrap site
* PV_intensity: Sum of residence times for the piling vessel per kilometer squared per hour relative to piling
* OWF: Windfarm ID (i.e. Beatrice, Moray East)

### Benhemma-Le_Gall_MMMP_BBL_short-term_ST_2017-19_HRP.txt

* Deployment_no: SoundTrap deployment number
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* Posix.nextmin: Date and time of broadband noise levels recorded (dd/mm/yyyy hh:mm:ss)
* broadband_SPL: Broadband Sound Pressure Levels (dB re 1 μPa) recorded by calibrated SoundTraps
* turbine: Wind turbine ID
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* bout_12hr: Piling bout ID per piling campaign
* piling_BA: Presence/absence of piling activities
* bout_interval_days: Time interval between piling bouts (in days)
* start_HRP: Start date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* end_HRP: End date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* dist.ST.turb.km: Distance between the Sountrap and turbine/piling location (in km)
* Location: SoundTrap site ID
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## OUTPUT DATASETS

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### Benhemma-Le_Gall_MMMP_Allocating_HRP_Before_piling_for_all_turbines_BOWL_2017.txt

### Benhemma-Le_Gall_MMMP_Allocating_HRP_Before_piling_for_all_turbines_MEOW_2019.txt

* NAME: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* turbine: Wind turbine ID
* bout_12hr: Piling bout ID
* start_bout: Start date and time of each piling bout (dd/mm/yyyy hh:mm:ss)
* end_bout: End date and time of each piling bout (dd/mm/yyyy hh:mm:ss)
* n_bout: number of piling bout for each piling location
* bout_duration: Piling bout duration (in hours)
* HRP: Hour Relative to Piling (HRP) (between -48 and 0)
* start_HRP: Start date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* end_HRP: End date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* interval: Time difference between the end and start of HRP (in hours)
* bout_interval_days: Time interval between consecutive piling bouts (in days)

### Benhemma-Le_Gall_MMMP_Allocating_hours_before_piling_bout_2017_BOWL.txt

### Benhemma-Le_Gall_MMMP_Allocating_hours_before_piling_bout_2019-20_MEOW.txt

* Posix: Date and time within each Hour Relative to Piling (dd/mm/yyyy hh:mm:ss)
* turbine: Wind turbine ID
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* bout_12hr: Piling bout ID per piling campaign
* piling_BA: Presence/absence of piling activities
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
### Benhemma-Le_Gall_MMMP_BOWL_time_of_arrival_RUAN_DPR.txt

### Benhemma-Le_Gall_MMMP_MEOW_time_of_arrival_JackingUp_DPR.txt

* Posix: Date and time of the Activity end (dd/mm/yyyy hh:mm:ss)
* Location: Piling vessel location
* act.start: Date and time of the Activity start (dd/mm/yyyy hh:mm:ss)
* Activity: Activity type ( i.e. Run Anchors at Beatrice, Jacking-up at Moray East)
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* bout_12hr: Piling bout ID per piling campaign
* start_bout: Date and time of the piling bout start (dd/mm/yyyy hh:mm:ss)
* time_of_arrival: Estimated arrival time of piling vessel (in hours)

### Benhemma-Le_Gall_MMMP_raw_data_HRP_vessel_intensity_GAM_without_PV_some_locations_removed.txt

* Deployment.no: CPOD deployment number
* Location.ID: CPOD site ID
* bout_12hr: Piling bout ID per piling campaign
* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* Turbine_Before: Wind turbine ID (unique to the windfarm; BE- for Beatrice, ME- for Moray East)
* year: Data collection year (yyyy)
* DPM.hour: Number of minutes within an hour, during which porpoise echolocation clicks were detected
* MinsOn_hour: Number of minutes logging data per hour
* n: Number of data summarised by site and hour
* prop_DPH: Proportion of minutes within an hour with porpoise echolocolation clicks logged
* start_HRP: Start date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* end_HRP: End date and time of each hour relative of piling (dd/mm/yyyy hh:mm:ss)
* porp.occ: Presence/Absence of porpoise echocolation clicks per hour
* Depl_loc: CPOD deployment number and site ID
* n_boat: Number of AIS-vessels within a 5 km buffer around the CPOD site per hour relative to piling
* n_AIS_dot: Number of 5-min interpolated AIS dots within a 5 km buffer around the CPOD site per hour relative to piling
* duration_min: Cumulative vessel duration (min) within a 5 km buffer area around CPOD site per hour relative to piling
* min_dist: Minimum distance (per HRP) between CPOD site and AIS vessels passing within a 5 km buffer area around that CPOD site
* mean_dist: Mean distance (per HRP) between CPOD site and AIS vessels passing within a 5 km buffer area around that CPOD site
* boat_density: Number of individual AIS-vessels per kilometer squared per hour relative to piling
* boat_intensity: Sum of residence times for all AIS-vessels per kilometer squared per hour relative to piling
* OWF: Windfarm ID (i.e. Beatrice, Moray East)
* dist_POD_turb.km: distance between the CPOD deployment site and the turbine/piling location (in km)
* sqrt.boat_intensity: Squared-root transformation of the vessel intensity metric

### Benhemma-Le_Gall_MMMP_pred_porpoise_occurrence_per_HRP_without_PV_some_locations_removed.txt

* Before_48h: Hour Relative to Piling (HRP) (between -48 and 0)
* OWF: Windfarm ID (i.e. Beatrice, Moray East)
* fit: Estimated probability of porpoise occurrence per HRP and windfarm
* se: Estimated standard error
* upper: Upper 95% confidence interval
* lower: Lower 95% confidence interval
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