Primary tabs

Researchers and analysts in Marine Scotland often use coding to solve analytical tasks and modelling. This group contains code that has been released as a package that can be used by others.
Please note that in most cases, this will be packages of functions or scripts that can be applied in an existing software package, rather than a full software solution.

License

UK Open Government Licence (OGL)

Other Access

The information on this page (the dataset metadata) is also available in these formats.

JSON RDF

via the DKAN API

Interim Population Consequences of Disturbance (iPCoD) Code Update - Version 3

The Interim Population Consequences of Disturbance (iPCoD) framework was developed by SMRU Consulting and the University of St Andrews in 2013 to forecast the potential effects on marine mammal populations in UK waters of any disturbance, hearing damage or collisions that might result from the construction or operation of offshore renewable energy devices.
A detailed description of the approach can be found in Harwood et al. (2013) and King et al. (2015). The iPCoD framework was designed to cope with the current situation, in which there is only limited knowledge about the potential effects of these developments on marine mammals. It should be recognised that it is very much an interim solution to the evaluation of these effects, and that there remains an urgent need for additional scientific research to address the knowledge gaps that were identified by Harwood et al. (2014).
Since its initial release (v1.0) in February 2014 on the Marine Scotland website: http://data.marine.gov.scot/dataset/protocol-implementing-interim-popula..., the tool was updated with amendments to the code and helpfiles in October 2014 (v1.1). Since then, the iPCoD tool has been used for a number of offshore wind developments in Germany, Netherlands, France and the UK (and possibly others) and has been used to explore the potential population level effects of collisions of a range of species with marine renewable energy devices in Scotland and Wales. Also during this time, SMRU Consulting and John Harwood have explored developing the tool further to improve the model framework.
Since the release of v1.1 there have been several internal iterations of the code (leading to a version 2). This release marks a significant material increase in the efficiency and capability of the interim PCoD framework (version 3).
References:
Harwood, J., S. King, R. Schick, C. Donovan & C. Booth 2013. A Protocol for Implementing the Interim Population Consequences of Disturbance (PCoD) Approach: Quantifying and Assessing the Effects of UK Offshore Renewable Energy Developments on Marine Mammal Populations. Scottish Marine and Freshwater Science 5(2). <http://www.gov.scot/Resource/0044/00443360.pdf >

Harwood, J. and King, S.L. (2017). The Sensitivity of UK Marine Mammal Populations to Marine Renewables Developments - Revised Version. Report number SMRUC-MSS-2017-005. King, S. L., Schick, R. S., Donovan, C., Booth, C. G., Burgman, M., Thomas, L., et al. (2015). An interim framework for assessing the population consequences of disturbance. Methods in Ecology and Evolution, 6(10), 1150e1158. http://dx.doi.org/10.1111/2041-210X.12411

doi: 
10.7489/1995-1
Citation: 
SMRU consulting, University of St. Andrews, and Marine Scotland. 2017. Interim Population Consequences of Disturbance (iPCoD) Code Update - Version 3. doi: 10.7489/1995-1

Data and Resources

FieldValue
Publisher
Modified Date
2017-10-04
Release Date
2017-10-04
Identifier
ea71eda6-f809-4b43-8e52-6133f891efb1
Language
English (United Kingdom)
License
UK Open Government Licence (OGL)
Data Dictionary

This update to the tool (version 3) comprises a number of improvements/developments, which are described below:
Improvements to run-time:
Run-times with version 2 of ~100x faster than original code are achievable, allowing users to consider many more development scenarios/parameter combinations and run more simulations to improve consistency.

Persistence of disturbance effects with range:
Version 2 includes increased flexibility in the way the effects of the persistence of disturbance (residual days of disturbance) are modelled, including a provision to specify different effects for animals close to the noise source and those further away (e.g. animals close to the pile may be disturbed for longer than animals further away). This has been explored in Booth et al (2017) – which provides some background to the approach and the capability which is available in v3.

Simplified data entry:
In version 2 it is now easier to prepare the data entry required for piling files. These can now start on 1 January for each year, rather than the start of the breeding season for the marine mammal species under consideration making it easier to build the schedule of piling for a development.

There are also a number of smaller improvements to other model specific elements:
• Minor bugs that caused unexpected crashes/error messages in the program fixed (although none of these affected model predictions)
• Ability to include density dependence if appropriate data are available
• Improved modelling of the effects of demographic stochasticity, thus avoiding occasional situations where the effects of disturbance appear to be positive.
• Modification in the way the effects of “moderate” disturbance on survival or birth rate is calculated. The v1 software used the mid-point in the range of effects on survival or birth rate predicted by the expert elicitation to calculate the effects of disturbance on all animals that experience “moderate” levels. This resulted in a potential overestimation of effects if most animals experience relatively small amounts of disturbance and underestimation of effects if most animals experience relatively large amounts. Version 2 is now implemented such that it uses the mean number of days of disturbance to calculate the effects of “moderate” disturbance, and therefore avoids these biases.

The tool comes with a new and extremely detailed helpfile to help users with the routine operation of the interim PCoD framework, also covering known error messages to aid usage of the model and getting past the most common mistakes in preparation to run PCoD scenarios.

Contact Name
Marine Scotland
Contact Email
Public Access Level
Public