# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "poems" in publications use:' type: software license: GPL-3.0-only title: 'poems: Pattern-Oriented Ensemble Modeling System' version: 1.3.1 doi: 10.1111/2041-210X.13720 identifiers: - type: doi value: 10.32614/CRAN.package.poems abstract: 'A framework of interoperable R6 classes (Chang, 2020, ) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, ). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, ); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, ), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.' authors: - family-names: Haythorne given-names: Sean email: sean.haythorne@unimelb.edu.au - family-names: Fordham given-names: Damien email: damien.fordham@adelaide.edu.au - family-names: Brown given-names: Stuart email: stuart.brown@sa.gov.au orcid: https://orcid.org/0000-0002-0669-1418 - family-names: Buettel given-names: Jessie email: jessie.buettel@utas.edu.au - family-names: Brook given-names: Barry email: barry.brook@utas.edu.au - family-names: Pilowsky given-names: July email: pilowskyj@caryinstitute.org orcid: https://orcid.org/0000-0002-6376-2585 preferred-citation: type: article title: 'poems: R package for simulating species'' range dynamics using pattern-oriented validation' authors: - family-names: Fordham given-names: Damien email: damien.fordham@adelaide.edu.au - family-names: Haythorne given-names: Sean email: sean.haythorne@unimelb.edu.au - family-names: Brown given-names: Stuart email: stuart.brown@sa.gov.au orcid: https://orcid.org/0000-0002-0669-1418 - family-names: Buettel given-names: Jessie email: jessie.buettel@utas.edu.au - family-names: Brook given-names: Barry email: barry.brook@utas.edu.au journal: Methods in Ecology and Evolution volume: '12' issue: '12' keywords: - distribution - extinction risk - metapopulation - pattern-oriented modelling - population dynamics - population viability analysis - range shift - spatially explicit population model doi: 10.1111/2041-210X.13720 url: https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13720 abstract: Abstract Spatially explicit population models (SEPMs) can simulate spatiotemporal changes in species' range dynamics in response to variation in climatic and environmental conditions, and anthropogenic activities. When combined with pattern-oriented modelling methods, ecological processes and drivers of range shifts and extinctions can be identified, and plausible chains of causality revealed. The open-source multi-platform R package poems provides functionality for simulating and validating projections of species' range dynamics using stochastic, lattice-based population models. Built-in modules allow parameter uncertainty to propagate through to model simulations, with their effects on species' range dynamics evaluated using Approximate Bayesian Computation. These validation procedures identify models with the structural complexity and parameterisation needed to simulate the effects of past changes in climate, environment and human activities on species' range shifts and extinction risk. We illustrate the features and versatility of poems by simulating the historical decline and extinction of the Thylacine Thylacinus cynocephalus, an icon of recent extinctions in Australia. We show that poems can reveal likely ecological pathways to extinction using pattern-oriented methods, providing validated projections of the range collapse and population decline of threatened species. By providing flexible and extendable modules for building and validating SEPMs of species' range dynamics, poems allows the effects of past and future threats on species' populations to be quantified using well-parameterised, structurally realistic models, with important generative mechanisms. Since poems can directly unravel ecological processes of species responses to global change, and strengthen predictions of range shifts and extinction risk—within a flexible, R-based environment—we anticipate that poems will be of significant value to ecologists, conservation managers and biogeographers. year: '2021' start: 2364-2371 repository: https://globalecologylab.r-universe.dev repository-code: https://github.com/GlobalEcologyLab/poems commit: 0a34aff37097d23b1e80522f42fc00066a0a1b97 url: https://globalecologylab.github.io/poems/ contact: - family-names: Pilowsky given-names: July email: pilowskyj@caryinstitute.org orcid: https://orcid.org/0000-0002-6376-2585