• IMAS Metadata Catalogue
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Southern elephant seal DEB-IBM (PLoS)

This meta data describes the raw output of the SES DEB-IBM built in NetLogo (version 6.0.1, March 2017; available from http://modelingcommons.org/browse/one_model/5348 ). The raw output consists of .csv files from several model runs. The detailed explanation of the model workings and background are published in Goedegebuure et al. (2018, PLoS ONE; Modelling southern elephant seals Mirounga leonina using an individual-based model coupled with a dynamic energy budget; DOI: 10.1371/journal.pone.0194950). In short: we developed an individual-based model which is coupled with a dynamic energy budget (a DEB-IBM) for southern elephant seals to demonstrate a method for detailed representation of marine mammals. We aimed to develop a model which could i) simulate energy use and life histories, as well as breeding traits of southern elephant seals in an emergent manner, ii) project a stable population over time, and iii) have realistic population dynamics and structure based on emergent life history features (such as age at first breeding, lifespan, fecundity and (yearling) survival). We evaluated the model's ability to represent a stable population over long time periods (> 10 generations), including the sensitivity of the emergent properties to variations in key parameters. The model was developed using life history data of female southern elephant seals from Macquarie Island and follows individuals from birth to death.

The information collected in the raw output are the same for the baseline model (stable, and with standard parameters), and the modified models to test for 1) low, and 2) high food availability, 3) low, and 4) high weaning thresholds (energetic level at which pups transition to juveniles), 5) low, and 6) high puberty thresholds (energetic level at which juveniles transition to physically mature adults). As well as recording the parameter values as set in the model, each .csv file records:

1) run number (usually 1-10)

2) step (time step, days)

3) min age at first breeding (years)

4) min age of adult

5) mean age of adult

6) mean age of juvenile

7) max age of individuals

8) max number of pups per female

9) fecundity

10) max size of individuals

11) mean size of adults

12) mean size of juveniles

13) total count of modelled population

14) total count of embryos

15) total count of pups

16) total count of yearlings

17) total count of juveniles (includes yearlings)

18) total count of adults

19) mean food availability of independent individuals (those not reliant on their mother) that are not fasting/moulting

20) carrying capacity (or expected equilibrium)

21) seed

NB. NetLogo calls individuals within the model turtles - thus output will mention turtles. Stages are as follows 0 = foetus, 1 = pup, 2 = juvenile, 3 = adult. Status are as follows, 0 = dependent on mother, 1 = fasting, 2 = foraging.

Simple

Identification info

Date (Creation)
2017-11-28
Date (Publication)
2018-03-21
Citation identifier
doi:10.4226/77/5ab1cc3f83ca4

Title
Information and documentation - Digital object identifier system
Date (Publication)
2018-03-21
Citation identifier
ISO 26324:2012

Citation identifier
https://doi.org/10.4226/77/5ab1cc3f83ca4

Principal investigator

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - Goedegebuure, Merel
Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS)
Private Bag 129
Hobart
Tasmania
7001
Australia
ORCID ID >

Credit
This study was supported by the Australian Government's Cooperative Research Centres Programme through the Antarctic Climate and Ecosystem Cooperative Research Centre, the Institute for Marine and Antarctic Studies, through the Australian Antarctic Science Program, project #4347, and through an Australian Government Research Training Program Scholarship.
Status
On going

Principal investigator

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - Goedegebuure, Merel
Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS)
Private Bag 129
Hobart
Tasmania
7001
Australia
ORCID ID >

Topic category
  • Biota
N
S
E
W


Temporal extent

Time period
2014-03-01
Maintenance and update frequency
As needed
Keywords (Theme)
  • Ecosystem models
  • individual-based model
  • dynamic energy budget theory
  • bioenergetics
  • end-to-end ecosystem model
Keywords (Taxon)
  • southern elephant seal
  • Mirounga leonina
NASA/GCMD Keywords, Version 8.5
  • EARTH SCIENCE | BIOSPHERE | ECOSYSTEMS | MARINE ECOSYSTEMS
  • EARTH SCIENCE | BIOLOGICAL CLASSIFICATION | ANIMALS/VERTEBRATES | MAMMALS | CARNIVORES | SEALS/SEA LIONS/WALRUSES
  • EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | SPECIES LIFE HISTORY
  • EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | SPECIES PREDATION
Australian and New Zealand Standard Research Classification (ANZSRC): Fields of Research
  • Behavioural Ecology
  • Marine and Estuarine Ecology (incl. Marine Ichthyology)

Resource constraints

Classification
Unclassified

Resource constraints

Use limitation
The data described in this record are the intellectual property of the University of Tasmania through the Institute for Marine and Antarctic Studies.

Resource constraints

Linkage
http://i.creativecommons.org/l/by/4.0/88x31.png

License Graphic

Title
Creative Commons Attribution 4.0 International License


>

Website
http://creativecommons.org/licenses/by/4.0/

License Text

Other constraints
Cite data as: Goedegebuure, M. (2017), Southern elephant seal DEB-IBM (PLoS). Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS). doi:10.4226/77/5ab1cc3f83ca4
Language
English
Character encoding
UTF8

Distribution Information

Distribution format
  • CSV files (.csv)

    File decompression technique
    Multiple files - zipped (.zip)

OnLine resource
DOWNLOAD RAW MODEL OUTPUT [~300MB .zip]

Resource lineage

Statement
The model was developed in NetLogo (version 6.0.1; Wilensky 1999; https://ccl.northwestern.edu/netlogo/) with data collected from female southern elephant seals from Macquarie Island (see e.g. McMahon et al 2005; Mar Ecol Prog Ser 288, p273-283). The SES DEB-IBM was modified from a DEB-IBM developed for water fleas, by Martin et al (2012; Methods Ecol Evol 3(2) p 445-449) using energetics data collated through DEBtool (http://www.debtheory.org/wik/). The raw data presented here (.csv files) are analysed using R (R Core Team 2017; https://www.R-project.org/). The first 50 years of the data are discarded as this is the run-in period of the model, and may not accurately represent the actual model run. For each parameter selected, the mean (or min, or max, as required) value has been taken for each run over the selected time frame (100 years), from which then the relevant analyses are done. Data is collected on a daily time-step from the model, over 180 years, where each year consists of 360 days (i.e. 12 x 30 days).
Hierarchy level
Dataset

mdb:MD_Metadata

Metadata identifier
28b3ce9f-ad5d-402b-93b7-cdd771e00630

Language
English
Character encoding
UTF8

Author

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - Goedegebuure, Merel

Point of contact

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - IMAS Data Manager

Type of resource

Resource scope
Dataset
Metadata linkage
https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/28b3ce9f-ad5d-402b-93b7-cdd771e00630

Point of truth URL of this metadata record

Date info (Creation)
2021-04-13T15:29:50
Date info (Revision)
2021-04-13T15:29:50

Metadata standard

Title
ISO 19115-3:2018
 
 

Overviews

Spatial extent

N
S
E
W


Keywords

Ecosystem models bioenergetics dynamic energy budget theory end-to-end ecosystem model individual-based model
Australian and New Zealand Standard Research Classification (ANZSRC): Fields of Research
Behavioural Ecology Marine and Estuarine Ecology (incl. Marine Ichthyology)
NASA/GCMD Keywords, Version 8.5
EARTH SCIENCE | BIOLOGICAL CLASSIFICATION | ANIMALS/VERTEBRATES | MAMMALS | CARNIVORES | SEALS/SEA LIONS/WALRUSES EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | SPECIES LIFE HISTORY EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | SPECIES PREDATION EARTH SCIENCE | BIOSPHERE | ECOSYSTEMS | MARINE ECOSYSTEMS

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