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 adult5) mean age of adult6) mean age of juvenile7) max age of individuals8) max number of pups per female9) fecundity10) max size of individuals11) mean size of adults12) mean size of juveniles13) total count of modelled population14) total count of embryos15) total count of pups16) total count of yearlings17) 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/moulting20) 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.

本元数据描述了基于NetLogo（版本6.0.1，2017年3月；可从http://modelingcommons.org/browse/one_model/5348获取）开发的SES DEB-IBM模型的原始输出。原始输出包含多次模型运行生成的.csv格式文件。该模型的运行机制与背景细节已发表于Goedegebuure等人（2018年，《公共科学图书馆·综合》(PLoS ONE)；《基于耦合动态能量收支的个体基模型模拟南象海豹（Mirounga leonina）》；DOI: 10.1371/journal.pone.0194950）。

简言之，我们开发了一款耦合动态能量收支的个体基模型（individual-based model），用于模拟南象海豹，以展示一种精细化表征海洋哺乳动物的方法。本研究旨在构建一款能够：i）以涌现性方式模拟南象海豹的能量利用、生活史以及繁殖性状；ii）随时间推移维持稳定种群；iii）基于涌现性生活史特征（如首次繁殖年龄、寿命、繁殖力和一龄幼崽存活率）呈现符合现实的种群动态与结构。我们评估了该模型在长周期（>10代）内维持稳定种群的能力，包括涌现特性对关键参数变化的敏感性。本模型基于麦夸里岛雌性南象海豹的生活史数据开发，追踪个体从出生到死亡的全生命周期。

原始输出中收录的信息，适用于基准模型（参数标准、种群稳定）以及用于测试以下变量的修改后模型：1）低食物可获得性、2）高食物可获得性；3）低断奶阈值（幼崽转变为幼体的能量水平）、4）高断奶阈值；5）低青春期阈值（幼体转变为物理成熟成体的能量水平）、6）高青春期阈值。除记录模型中设置的参数值外，每个.csv格式文件还包含以下字段：1）运行编号（通常为1-10）；2）步长（时间步，单位：天）；3）首次繁殖的最小年龄（单位：年）；4）成体最小年龄；5）成体平均年龄；6）幼体平均年龄；7）个体最大年龄；8）单只雌性的最大产仔数；9）繁殖力；10）个体最大体型；11）成体平均体型；12）幼体平均体型；13）模拟种群总数量；14）胚胎总数量；15）幼崽总数量；16）一龄幼崽总数量；17）幼体总数量（包含一龄幼崽）；18）成体总数量；19）独立个体（不依赖母兽）且未处于禁食/换毛阶段的个体的平均食物可获得性；20）承载能力（或预期平衡种群规模）；21）初始种群规模。

注：NetLogo将模型内的个体称为turtles（龟），因此输出文件中会提及turtles。生命阶段定义如下：0=胚胎，1=幼崽，2=幼体，3=成体。个体状态定义如下：0=依赖母兽，1=禁食，2=觅食。