Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
This manuscript introduces trident, an R package for performing dental microwear texture analysis and subsequently classifying variables based on their ability to separate discrete categories. Dental microwear textures reflect the physical properties of the food, the feeding ecology of a given speci...
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2024-09-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.467/ |
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| author | Thiery, Ghislain Francisco, Arthur Louail, Margot Berlioz, Emilie Blondel, Cécile Brunetière, Noël Ramdarshan, Anusha Walker, Axelle EC Merceron, Gildas |
| author_facet | Thiery, Ghislain Francisco, Arthur Louail, Margot Berlioz, Emilie Blondel, Cécile Brunetière, Noël Ramdarshan, Anusha Walker, Axelle EC Merceron, Gildas |
| author_sort | Thiery, Ghislain |
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| description | This manuscript introduces trident, an R package for performing dental microwear texture analysis and subsequently classifying variables based on their ability to separate discrete categories. Dental microwear textures reflect the physical properties of the food, the feeding ecology of a given species, and niche partitioning when considering multi-specific communities. The trident package comes with independent functions and a user interface, trident, enabling easy and fast proficiency. It can import .SUR files, then remove aberrant peaks and possibly polynomial surfaces. Next, it can measure up to 24 texture parameters and their statistics of heterogeneity, generating 384 variables. It also ranks any number of variables using five different methods, displays the results in multivariate analyses, and exports the results into R, providing access to its large asset of libraries. We then present these features in three case studies, showing how trident helps answer questions commonly investigated by paleontologists and archaeologists. In the first case study, we separate four groups of domestic pigs based on their dietary composition. In the second case study, we identify microwear texture patterns in a large database of 15 primate species and relate these patterns to biomechanical and ecological factors. The third case study investigates the dental microwear textures of four extant ruminants to infer the diet of an extinct antelope from the Pleistocene of Greece. These case studies show how trident can leverage dental microwear texture analysis results. |
| format | Article |
| id | doaj-art-35faf2f7ba5e43c1bd557663fa6184b3 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | Peer Community In |
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| series | Peer Community Journal |
| spelling | doaj-art-35faf2f7ba5e43c1bd557663fa6184b32025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-09-01410.24072/pcjournal.46710.24072/pcjournal.467Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis Thiery, Ghislain0https://orcid.org/0000-0003-4789-7372Francisco, Arthur1Louail, Margot2https://orcid.org/0000-0002-9927-4508Berlioz, Emilie3https://orcid.org/0000-0002-2694-8436Blondel, Cécile4https://orcid.org/0000-0002-7022-6959Brunetière, Noël5https://orcid.org/0000-0003-4730-6931Ramdarshan, Anusha6Walker, Axelle EC7Merceron, Gildas8https://orcid.org/0000-0001-5777-7126Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, FranceInstitut PPRIME : Recherche et Ingénierie en Matériaux, Mécanique et Energétique [UPR 3346], SP2MI Téléport 2 Boulevard Pierre et Marie Curie, BP 3017986962 FUTUROSCOPE CEDEXLaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, France; Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA 02138, USALaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, France; Grupo I+D+i de Evolución Humana y Adaptaciones durante la Prehistoria = Research Group on Human Evolution and Adaptations during the Prehistory, Universidad de Cantabria, Dpto. Ciencias Históricas, Av. Los Castros 44, 39005 Santander, EspañaLaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, FranceInstitut PPRIME : Recherche et Ingénierie en Matériaux, Mécanique et Energétique [UPR 3346], SP2MI Téléport 2 Boulevard Pierre et Marie Curie, BP 3017986962 FUTUROSCOPE CEDEXLaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, FranceLaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, FranceLaboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie [UMR 7262], Université de Poitiers, Bâtiment B35, TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, FranceThis manuscript introduces trident, an R package for performing dental microwear texture analysis and subsequently classifying variables based on their ability to separate discrete categories. Dental microwear textures reflect the physical properties of the food, the feeding ecology of a given species, and niche partitioning when considering multi-specific communities. The trident package comes with independent functions and a user interface, trident, enabling easy and fast proficiency. It can import .SUR files, then remove aberrant peaks and possibly polynomial surfaces. Next, it can measure up to 24 texture parameters and their statistics of heterogeneity, generating 384 variables. It also ranks any number of variables using five different methods, displays the results in multivariate analyses, and exports the results into R, providing access to its large asset of libraries. We then present these features in three case studies, showing how trident helps answer questions commonly investigated by paleontologists and archaeologists. In the first case study, we separate four groups of domestic pigs based on their dietary composition. In the second case study, we identify microwear texture patterns in a large database of 15 primate species and relate these patterns to biomechanical and ecological factors. The third case study investigates the dental microwear textures of four extant ruminants to infer the diet of an extinct antelope from the Pleistocene of Greece. These case studies show how trident can leverage dental microwear texture analysis results.https://peercommunityjournal.org/articles/10.24072/pcjournal.467/Diet inferenceDMTAMultivariate analysis |
| spellingShingle | Thiery, Ghislain Francisco, Arthur Louail, Margot Berlioz, Emilie Blondel, Cécile Brunetière, Noël Ramdarshan, Anusha Walker, Axelle EC Merceron, Gildas Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis Peer Community Journal Diet inference DMTA Multivariate analysis |
| title | Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
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| title_full | Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
|
| title_fullStr | Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
|
| title_full_unstemmed | Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
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| title_short | Introducing ‘trident’: a graphical interface for discriminating groups using dental microwear texture analysis
|
| title_sort | introducing trident a graphical interface for discriminating groups using dental microwear texture analysis |
| topic | Diet inference DMTA Multivariate analysis |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.467/ |
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