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

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 ..., 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., , # 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_di...