Demes: a standard format for demographic models
Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth ra...
| المؤلفون الرئيسيون: | , , , , |
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| التنسيق: | Journal article |
| اللغة: | English |
| منشور في: |
Oxford University Press
2022
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| _version_ | 1826308834286632960 |
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| author | Gower, G Ragsdale, AP Bisschop, G Kelleher, J Et al. |
| author_facet | Gower, G Ragsdale, AP Bisschop, G Kelleher, J Et al. |
| author_sort | Gower, G |
| collection | OXFORD |
| description | Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field. In particular, the important task of translating the model descriptions in published work into input suitable for population genetic simulators is labor intensive and error prone. We propose the Demes data model and file format, built on widely used technologies, to alleviate these issues. Demes provide a well-defined and unambiguous model of populations and their properties that is straightforward to implement in software, and a text file format that is designed for simplicity and clarity. We provide thoroughly tested implementations of Demes parsers in multiple languages including Python and C, and showcase initial support in several simulators and inference methods. An introduction to the file format and a detailed specification are available at https://popsim-consortium.github.io/demes-spec-docs/. |
| first_indexed | 2024-03-07T07:25:13Z |
| format | Journal article |
| id | oxford-uuid:02c3bafd-b057-455a-960e-c76d7b6dcf51 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:25:13Z |
| publishDate | 2022 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:02c3bafd-b057-455a-960e-c76d7b6dcf512022-11-11T13:04:55ZDemes: a standard format for demographic modelsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:02c3bafd-b057-455a-960e-c76d7b6dcf51EnglishSymplectic ElementsOxford University Press2022Gower, GRagsdale, APBisschop, GKelleher, JEt al.Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field. In particular, the important task of translating the model descriptions in published work into input suitable for population genetic simulators is labor intensive and error prone. We propose the Demes data model and file format, built on widely used technologies, to alleviate these issues. Demes provide a well-defined and unambiguous model of populations and their properties that is straightforward to implement in software, and a text file format that is designed for simplicity and clarity. We provide thoroughly tested implementations of Demes parsers in multiple languages including Python and C, and showcase initial support in several simulators and inference methods. An introduction to the file format and a detailed specification are available at https://popsim-consortium.github.io/demes-spec-docs/. |
| spellingShingle | Gower, G Ragsdale, AP Bisschop, G Kelleher, J Et al. Demes: a standard format for demographic models |
| title | Demes: a standard format for demographic models |
| title_full | Demes: a standard format for demographic models |
| title_fullStr | Demes: a standard format for demographic models |
| title_full_unstemmed | Demes: a standard format for demographic models |
| title_short | Demes: a standard format for demographic models |
| title_sort | demes a standard format for demographic models |
| work_keys_str_mv | AT gowerg demesastandardformatfordemographicmodels AT ragsdaleap demesastandardformatfordemographicmodels AT bisschopg demesastandardformatfordemographicmodels AT kelleherj demesastandardformatfordemographicmodels AT etal demesastandardformatfordemographicmodels |