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Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance

Cite this dataset

Chudzinska, Magda; Klementisova, Katarina; Booth, Cormac; Harwood, John (2023). Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance [Dataset]. Dryad. https://doi.org/10.5061/dryad.v41ns1s35

Abstract

We developed dynamic bioenergetics models to investigate how behavioural responses to anthropogenic disturbance events might affect the population dynamics of three marine mammal species (harbour porpoise, grey seal and harbour seal) with contrasting life-history traits (capital vs income breeders) and movement behaviour (resident vs nomadic). We used these models to analyse how individual vital rates were affected by differences in the probability of disturbance and the duration of any behavioural response, while taking account of uncertainty in the model parameters and heterogeneity in behaviour. The outputs of individual movement models and telemetry data were then used to determine how the probability of exposure might vary among species, individuals, and geographical locations. We then demonstrate how these estimated probabilities of exposure can be translated into probabilities of disturbance. For illustrative purposes, we modelled the potential effects of a temporary decrease in energy assimilation associated with a series of disturbance events that might realistically occur during the construction of an offshore windfarm. Offspring starvation mortality was the vital rate that was most affected by these disturbance events. Monitoring of rates should be considered as standard practice so that populations' responses can be detected as early as possible. Predicted effects on individual vital rates depended on the species’ movement behaviour and the likely density of animals where the modelled construction activity was assumed to take place. The magnitude of these effects also depended critically on the assumed duration of the reduction in energy assimilation. No direct estimates of this variable are currently available, but we suggest some ways in which it could be estimated. The described approach could be extended to other species and activities, given sufficient information to parameterise the component models. However, we emphasise the need to account for among-individual heterogeneities and uncertainties in the values of the many model parameters.

README: Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance

https://doi.org/10.5061/dryad.v41ns1s35

Description of the data and file structure

All the input files are also placed on GitHub. The link is provided here and in the paper.

https://github.com/MagdaChu/Chudzinska-et-al.-Bioenergetic-and-movement

The same data are copied here and provided as a zipped file. After unzipping, the inputs are structured in three folders.

1) 'Bioenergetic model'

This folder contains the bioenergetic models for the three species. See next section on how to use it. Note that there is no input data (e.g. a CSV file) required to run the model in the absence of disturbance. All the parameters have to be specified in the code.

2) '3D graph SI'

This folder contains code and input file to generate Figure E1 from the Supplementary Information. Please follow the instruction in the code to produce the graph.

The csv input pile has the following columns:

'Dist_effect' - effect of disturbance expressed as number of hours per day of no foraging

'p_dist' - probability of disturbance

xx_BirthRate; xx_CalfSurv; xx_AdSurv - percentage of birth rate, calf/pup survival and adult survival in comparison to no disturbance for the two studied species (xx): HP harbour porpoise, GS grey seal

'3) Movement'

This folder contains all input data and code to generate Figure 2 from the main paper. The input data are in RData format - format specific to R software. Please follow the instruction in the code produce the graph.

Once loaded to R, the input data have the following columns

'Group1' - animal ID

'Group2' - date

'low30P'; 'high30P' - proportion of day each tracked or modelled individual spent in the high or low density area.

Code/Software

The bioenergetic models are written in R software. The code has the same structure for each species. SpeciesDEB_Control.R and SpeciesDEB_Params.R are the only two code needed user input. The SpeciesDEB_params.R file contain the list of all parameters need to run the models. The values in the codes are the values used in the final simulations. To see the list and meaning of each parameter, refer to the Supplementary Information. In SpeciesDEB_Control.R code, the user can define the settings and parameters for the disturbance scenario. Follow the commented lines in the code for details. This is the main script to start the simulations.

Methods

The attached R code presents the bioenergetic model used in the study. No input data is needed for simulations other than defining model settings.

Pre-processed data from telemetry are also attached in order to produce Figure 2 in the manuscript. 

Finally, input data (generated from the bioenergetic model) and the code to produce Figure E1 in Supplementary Information os also included.

Funding

Marine Mammal Scientific Support Research Programme , Award: 19981

Naval Facilities Engineering Command, Award: N3943019C2175, Engineering and Expeditionary Warfare Center