Brief description
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.
Lineage
Maintenance and Update Frequency: asNeeded
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).
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).
Notes
CreditThis 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.
Data time period: 2014-03-01
text: westlimit=156.580078125; southlimit=-56.3627031396; eastlimit=161.94140625; northlimit=-52.7747758852
Subjects
ANIMALS/VERTEBRATES |
BIOLOGICAL CLASSIFICATION |
Biological Sciences |
BIOSPHERE |
Behavioural Ecology |
CARNIVORES |
EARTH SCIENCE |
EARTH SCIENCE | BIOSPHERE | ECOSYSTEMS | MARINE ECOSYSTEMS |
ECOLOGICAL DYNAMICS |
Ecology |
Ecosystem models |
MAMMALS |
Marine and Estuarine Ecology (Incl. Marine Ichthyology) |
Mirounga leonina |
SEALS/SEA LIONS/WALRUSES |
SPECIES LIFE HISTORY |
SPECIES PREDATION |
SPECIES/POPULATION INTERACTIONS |
bioenergetics |
biota |
dynamic energy budget theory |
end-to-end ecosystem model |
individual-based model |
southern elephant seal |
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Other Information
(DOWNLOAD RAW MODEL OUTPUT [~300MB .zip])
Identifiers
- global : 28b3ce9f-ad5d-402b-93b7-cdd771e00630
- DOI : 10.4226/77/5ab1cc3f83ca4
- DOI : https://doi.org/10.4226/77/5ab1cc3f83ca4
