This material and novel code is provided open access and peer review for the following manuscript: 

Modelling climate influences on male survival in the highly polygynous southern elephant seal (Mirounga leonina)
Article for submission in ecosphere (Subject Tract: Climate Ecology) 

Authors:
Volzke, Sophia; Cleeland, Jaimie B.; McMahon, Clive R.; Hindell, Mark A.; Corney, Stuart P. and Wotherspoon, Simon J.

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Last updated: October 2023



The main file to run is MPM-ModelSelection.Rmd
This is an RMarkdown file that will call all other resources provided within this folder. 

Additionally, this analysis requires downloading the elephant seal capture-mark-recapture data from Macquarie Island. [Filename:TAGS_ELLIE_SIGHTINGS.csv] 
This file is also openly available within the Data folder. 

Files and their purpose: 
HMM.Rmd: novel code for analysing matrix population model, including setup and simulation of a hidden markkov model, and functions for using scott's algortihm (Reference within) and running bootstrap (parametric/non-parametric) simulations

Model.Rmd: Visual illustration of the matrix population model structure

MPM-ModelSelection.Rmd: Main Analysis (model selection)

FOLDERS:
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Bootstrap Folder - includes code and html results of running bootstrap simulations. Parametric and non-parametric. Results saved and visualised within (parboot / nparboot.RData)


Data Folder - includes data and data manipulation files

* SAM.csv and SOI.csv: annual average Southern Annular Mode and Southern Oscillation Index, as aquired by the referenced sources (see publication)

* TagData.Rmd: Data manipulation, filtering and checking before preparing for analysis in encounter histories format of annual resights

* TAGS_ELLIE_SIGHTINGS.csv: Raw data file, see TAGS_ELLIE_SIGHTINGS_README.md for further info


NULL Folder - includes code and results of the null model. This model has slightly different structure due to not having any covariates within (no weaning mass, no climate covariates), altering the dimensions of the matrix calculation. The result gets manually entered into the AIC model selection table. All files within this folder are the null model equivalent of the MPM model.

Please contact Sophia Volzke (sophia.volzke@utas.edu.au) if you have any questions.