DOI: 10.5061/dryad.v41ns1s35
title: Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance

description: 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.
description: 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.
description: # Combining bioenergetics and movement models to improve understanding of
 the population consequences of disturbance
 ## 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.
 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.