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Chapman Hall\u002FCRC, 10.1201\u002F9781420010404",{"doi":461},"10.1201\u002F9781420010404",{"id":24,"text":463,"url":24,"identifiers":464},"Zuur, 2009a, Mixed Effects Models and Extensions in Ecology with R, 10.1007\u002F978-0-387-87458-6",{"doi":465},"10.1007\u002F978-0-387-87458-6",{"id":24,"text":467,"url":24,"identifiers":468},"Zuur, 2007, Analysing Ecological Data, 10.1007\u002F978-0-387-45972-1",{"doi":469},"10.1007\u002F978-0-387-45972-1",{"id":24,"text":471,"url":24,"identifiers":472},"Zuur, 2009b, A Beginner’s Guide to R, 10.1007\u002F978-0-387-93837-0",{"doi":473},"10.1007\u002F978-0-387-93837-0",false,{"id":476,"createTime":477,"updateTime":478,"relativeEntities":479,"slug":480,"properties":481,"entityType":165,"verifyStatus":166,"verifyTime":477,"verifyNote":167,"languages":494,"translateLanguages":24,"viewCount":25,"primaryUrl":495,"fullTextUrl":24,"authors":496,"publicationType":240,"publisherRelationship":633,"citationCount":25,"citationInfo":687,"publishDate":690,"publishYear":688,"citationAnalyzeStatus":23,"lastCitationAnalyze":691,"indexDatabases":692,"openAccess":24,"references":693,"isForceReanalyzing":474},"609201f2-7dc1-452e-8041-62fc9c204686","2024-09-29T21:28:50.761+00:00","2026-03-19T22:21:48.685+00:00",[],"Quantifying-apart-what-belongs-together-A-multi-state-species-distribution-modelling-framework-for-species-using-distinct-habitats",{"openalex":482,"mag":484,"abstract":486,"title":488,"gsPaper":490,"doi":492},{"VOID":483},"W2687052915",{"VOID":485},"2687052915",{"EN":487},"\u003Cjats:title>Abstract\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>Species distribution models (\u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content>s) have been used to inform scientists and conservationists about the status and change in occurrence patterns in threatened species. Many mobile species use multiple functionally distinct habitats, and cannot occupy one habitat type without the other being within a reachable distance. For such species, classical applications of \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content>s might lead to erroneous representations of habitat suitability, as the complex relationships between predictors are lost when merging occurrence information across multiple habitats. To better account for the spatial arrangement of complementary—yet mandatory—habitat types, it is important to implement modelling strategies that partition occurrence information according to habitat use in a spatial context. Here, we address this issue by introducing a multi‐state \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content> framework.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>The multi‐state \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content> framework stratifies occurrences according to the temporal or behavioural use of distinct habitat types, referred to as “states.” Multiple \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content>s are then run for each state and statistical thresholds of presence are used to combine these separate predictions. To identify suitable sites that account for distance between habitats, two optional modules are proposed where the thresholded output is aggregated and filtered by minimum area size, or through moving windows across maximum reachable distances.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>We illustrate the full use of this framework by modelling the dynamic terrestrial breeding habitat preferences of the New Zealand sea lion (\u003Cjats:styled-content style=\"fixed-case\">NZSL\u003C\u002Fjats:styled-content>) (\u003Cjats:italic>Phocarctos hookeri\u003C\u002Fjats:italic>), using Maxent and trialling both modules to identify suitable sites for possible recolonization.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>The Maxent predictions showed excellent performance, and the multi‐state \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content> framework highlighted 36–77 potential suitable breeding sites in the study area.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>This framework can be applied to inform management when defining habitat suitability for species with complex changes in habitat use. It accounts for temporal and behavioural changes in distribution, maintains the individuality of each partitioned \u003Cjats:styled-content style=\"fixed-case\">SDM\u003C\u002Fjats:styled-content>, and considers distance between distinct habitat types. It also yields one final, easy‐to‐understand output for stakeholders and managers.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>",{"EN":489},"Quantifying apart what belongs together: A multi‐state species distribution modelling framework for species using distinct habitats",{"VOID":491},"[\"507952034304311520\"]",{"VOID":493},"10.1111\u002F2041-210x.12847",[169],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002F2041-210X.12847",[497,526,553,572,591,608],{"id":498,"sortIndex":25,"researcher":24,"roles":499,"affiliations":500,"properties":517,"displayName":521,"givenName":24,"familyName":24},"1e68bc32-74f4-4374-9c0d-9b89a10919be",[],[501,509],{"id":502,"sortIndex":25,"affiliation":503,"properties":24},"5e872d2d-fbcc-4add-bc9d-a4469da582c5",{"id":502,"createTime":24,"updateTime":24,"relativeEntities":504,"slug":24,"properties":505,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":508,"statistic":24},[],{"title":506},{"VI":507},"Department of Wildlife Sciences, University of Göttingen, Göttingen, Germany",[],{"id":510,"sortIndex":188,"affiliation":511,"properties":24},"22e43c41-0915-42d1-9dec-c7d7d8923e45",{"id":510,"createTime":24,"updateTime":24,"relativeEntities":512,"slug":24,"properties":513,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":516,"statistic":24},[],{"title":514},{"EN":515},"Workgroup on Endangered Species University of Göttingen  Göttingen Germany",[],{"orcid":518,"title":520,"gsAuthor":522,"openalex":524},{"VOID":519},"https:\u002F\u002Forcid.org\u002F0000-0002-5634-3956",{"EN":521},"Veronica F. 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Variation along the significant axes can be mapped, used to draw biplots or interpreted through subsequent analyses, whilst the nonsignificant axes may be dropped from further consideration.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>2.\u003C\u002Fjats:bold> Three methods have been implemented in computer programs to test the significance of the canonical axes; they are compared in this paper. The simultaneous test of all individual canonical axes, which is appealing because of its simplicity, produced incorrect (highly inflated) levels of type I error for the axes following those corresponding to true relationships in the data, so it is invalid. The ‘marginal’ testing method implemented in the ‘vegan’ R package and the ‘forward’ testing method implemented in the program CANOCO were found to have correct levels of type I error and comparable power. Permutation of the residuals achieved greater power than permutation of the raw data.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>3.\u003C\u002Fjats:bold> R functions found in a Supplement to this paper provide the first formal description of the ‘marginal’ and ‘forward’ testing methods.\u003C\u002Fjats:p>",{"EN":884},"Testing the significance of canonical axes in redundancy analysis",{"VOID":886},"10.1111\u002Fj.2041-210x.2010.00078.x",[169],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002Fj.2041-210X.2010.00078.x",[890,909,928],{"id":891,"sortIndex":25,"researcher":24,"roles":892,"affiliations":893,"properties":902,"displayName":906,"givenName":24,"familyName":24},"37d5ccf1-1b41-466f-a99d-383d4a0b7312",[],[894],{"id":895,"sortIndex":25,"affiliation":896,"properties":24},"6d5dbc8c-6d85-4ff4-bd03-816b6205e070",{"id":895,"createTime":24,"updateTime":24,"relativeEntities":897,"slug":24,"properties":898,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":901,"statistic":24},[],{"title":899},{"VI":900},"Département de sciences biologiques, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada",[],{"orcid":903,"title":905,"openalex":907},{"VOID":904},"https:\u002F\u002Forcid.org\u002F0000-0002-3838-3305",{"EN":906},"Pierre Legendre",{"VOID":908},"A5071178128",{"id":910,"sortIndex":188,"researcher":24,"roles":911,"affiliations":912,"properties":921,"displayName":925,"givenName":24,"familyName":24},"04ed92ed-1b67-497d-bd08-da2e9d2a1227",[],[913],{"id":914,"sortIndex":25,"affiliation":915,"properties":24},"3cf612d9-33d6-4796-a619-34b14983982a",{"id":914,"createTime":24,"updateTime":24,"relativeEntities":916,"slug":24,"properties":917,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":920,"statistic":24},[],{"title":918},{"VI":919},"Department of Biology, University of Oulu, P.O. 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183",{},{"id":1107,"createTime":1108,"updateTime":1109,"relativeEntities":1110,"slug":1111,"properties":1112,"entityType":165,"verifyStatus":166,"verifyTime":1108,"verifyNote":167,"languages":1127,"translateLanguages":1128,"viewCount":25,"primaryUrl":1129,"fullTextUrl":24,"authors":1130,"publicationType":240,"publisherRelationship":1282,"citationCount":1337,"citationInfo":1338,"publishDate":1348,"publishYear":1339,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":1349,"openAccess":24,"references":1350,"isForceReanalyzing":474},"f4b93f03-efe6-4241-a304-e56e4e19e009","2024-12-02T21:11:40.544+00:00","2024-12-31T10:06:58.714+00:00",[],"-scp-ENM-scp-eval-An-R-package-for-conducting-spatially-independent-evaluations-and-estimating-optimal-model-complexity-for-scp-Maxent-scp-ecological-niche-models",{"openalex":1113,"mag":1115,"abstract":1117,"title":1120,"keywords":1123,"doi":1125},{"VOID":1114},"W2046577517",{"VOID":1116},"2046577517",{"VI":1118,"EN":1119},"\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>Các nghiên cứu gần đây đã chỉ ra rằng cần phải nâng cao độ chính xác trong việc xây dựng và đánh giá các mô hình sinh cảnh sinh thái (ENM) dựa trên dữ liệu có mặt chỉ. Hai mục tiêu chính là cân bằng tính phù hợp của mô hình với độ phức tạp của mô hình (ví dụ: bằng cách ‘điều chỉnh’ các cài đặt mô hình) và đánh giá các mô hình với dữ liệu độc lập theo không gian. Những vấn đề này đặc biệt quan trọng đối với các tập dữ liệu bị ảnh hưởng bởi thiên lệch trong việc lấy mẫu, và cho các nghiên cứu yêu cầu chuyển giao các mô hình qua không gian hoặc thời gian (ví dụ: phản ứng với biến đổi khí hậu hoặc sự lan truyền của các loài xâm hại). Việc thực hiện hiệu quả các quy trình để đạt được những mục tiêu này, tuy nhiên, yêu cầu phải tự động hóa.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Chúng tôi đã phát triển gói ENMeval, một gói R mà: (i) tạo ra các tập dữ liệu cho phép kiểm tra chéo k‐fold bằng một trong nhiều phương pháp phân chia dữ liệu có mặt (bao gồm các tùy chọn cho các phân chia độc lập theo không gian), (ii) xây dựng một loạt các mô hình ứng cử viên sử dụng Maxent với nhiều cài đặt do người dùng định nghĩa và (iii) cung cấp nhiều chỉ số đánh giá để hỗ trợ trong việc chọn cài đặt mô hình tối ưu. Sáu phương pháp để phân chia dữ liệu bao gồm jackknife n−1, k‐fold ngẫu nhiên (=bins), các fold do người dùng chỉ định và ba phương pháp phân chia theo cấu trúc địa lý có mặt. ENMeval định lượng sáu chỉ số đánh giá: diện tích dưới đường cong của đồ thị đặc điểm hoạt động của bộ thu cho các địa điểm thử nghiệm (AUC\u003Csub>TEST\u003C\u002Fsub>), sự khác biệt giữa AUC huấn luyện và AUC kiểm tra (AUC\u003Csub>DIFF\u003C\u002Fsub>), hai tỷ lệ thiếu sót cơ sở ngưỡng khác nhau cho các địa điểm thử nghiệm và tiêu chí thông tin Akaike điều chỉnh cho kích thước mẫu nhỏ (AIC\u003Csub>c\u003C\u002Fsub>).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Chúng tôi đã chứng minh ENMeval bằng cách điều chỉnh các cài đặt mô hình cho tám loài cây thuộc chi Coccoloba ở Puerto Rico dựa trên AIC\u003Csub>c\u003C\u002Fsub>. Các chỉ số đánh giá đã thay đổi đáng kể giữa các cài đặt mô hình, và các mô hình được chọn với AIC\u003Csub>c\u003C\u002Fsub> khác với các mô hình mặc định.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Tóm lại, ENMeval tạo điều kiện thuận lợi cho việc sản xuất các ENM tốt hơn và nên thúc đẩy nghiên cứu phương pháp trong tương lai về nhiều vấn đề nổi bật hiện có.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>Recent studies have demonstrated a need for increased rigour in building and evaluating ecological niche models (\u003Cjats:styled-content style=\"fixed-case\">ENM\u003C\u002Fjats:styled-content>s) based on presence‐only occurrence data. Two major goals are to balance goodness‐of‐fit with model complexity (e.g. by ‘tuning’ model settings) and to evaluate models with spatially independent data. These issues are especially critical for data sets suffering from sampling bias, and for studies that require transferring models across space or time (e.g. responses to climate change or spread of invasive species). Efficient implementation of procedures to accomplish these goals, however, requires automation.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>We developed \u003Cjats:styled-content style=\"fixed-case\">\u003Cjats:styled-content>ENM\u003C\u002Fjats:styled-content>\u003C\u002Fjats:styled-content>\u003Cjats:styled-content>eval\u003C\u002Fjats:styled-content>, an R package that: (i) creates data sets for \u003Cjats:italic>k\u003C\u002Fjats:italic>‐fold cross‐validation using one of several methods for partitioning occurrence data (including options for spatially independent partitions), (ii) builds a series of candidate models using \u003Cjats:sc>Maxent\u003C\u002Fjats:sc> with a variety of user‐defined settings and (iii) provides multiple evaluation metrics to aid in selecting optimal model settings. The six methods for partitioning data are \u003Cjats:italic>n\u003C\u002Fjats:italic>−1 jackknife, random \u003Cjats:italic>k\u003C\u002Fjats:italic>‐folds ( = bins), user‐specified folds and three methods of masked geographically structured folds. \u003Cjats:styled-content>ENM\u003C\u002Fjats:styled-content>\u003Cjats:styled-content>eval\u003C\u002Fjats:styled-content> quantifies six evaluation metrics: the area under the curve of the receiver‐operating characteristic plot for test localities (\u003Cjats:styled-content style=\"fixed-case\">AUC\u003Cjats:sub>TEST\u003C\u002Fjats:sub>\u003C\u002Fjats:styled-content>), the difference between training and testing \u003Cjats:styled-content style=\"fixed-case\">AUC\u003C\u002Fjats:styled-content> (\u003Cjats:styled-content style=\"fixed-case\">AUC\u003Cjats:sub>DIFF\u003C\u002Fjats:sub>\u003C\u002Fjats:styled-content>), two different threshold‐based omission rates for test localities and the Akaike information criterion corrected for small sample sizes (\u003Cjats:styled-content style=\"fixed-case\">AIC\u003C\u002Fjats:styled-content>c).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>We demonstrate \u003Cjats:styled-content>ENM\u003C\u002Fjats:styled-content>\u003Cjats:styled-content>eval\u003C\u002Fjats:styled-content> by tuning model settings for eight tree species of the genus \u003Cjats:italic>Coccoloba\u003C\u002Fjats:italic> in Puerto Rico based on \u003Cjats:styled-content style=\"fixed-case\">AIC\u003C\u002Fjats:styled-content>c. Evaluation metrics varied substantially across model settings, and models selected with \u003Cjats:styled-content style=\"fixed-case\">AIC\u003C\u002Fjats:styled-content>c differed from default ones.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>In summary, \u003Cjats:styled-content>ENMeval\u003C\u002Fjats:styled-content> facilitates the production of better \u003Cjats:styled-content style=\"fixed-case\">ENM\u003C\u002Fjats:styled-content>s and should promote future methodological research on many outstanding issues.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>",{"EN":1121,"VI":1122},"\u003Cscp>ENM\u003C\u002Fscp>eval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for \u003Cscp>Maxent\u003C\u002Fscp> ecological niche models","ENMeval: Một gói R để thực hiện các đánh giá độc lập theo không gian và ước lượng độ phức tạp mô hình tối ưu cho các mô hình sinh cảnh sinh thái Maxent",{"VI":1124},"",{"VOID":1126},"10.1111\u002F2041-210x.12261",[169],[171],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002F2041-210X.12261",[1131,1150,1169,1194,1211,1234,1251],{"id":1132,"sortIndex":25,"researcher":24,"roles":1133,"affiliations":1134,"properties":1143,"displayName":1147,"givenName":24,"familyName":24},"0f2a06b6-10c9-4af9-87b2-9873dfec2da2",[],[1135],{"id":1136,"sortIndex":25,"affiliation":1137,"properties":24},"0dddda9f-a7e1-4d91-9fe6-85683395e7da",{"id":1136,"createTime":24,"updateTime":24,"relativeEntities":1138,"slug":24,"properties":1139,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1142,"statistic":24},[],{"title":1140},{"EN":1141},"Department of Ecology, Evolution and Environmental Biology, Columbia University, 1200 Amsterdam Ave., New York, NY, 10027, USA",[],{"orcid":1144,"title":1146,"openalex":1148},{"VOID":1145},"https:\u002F\u002Forcid.org\u002F0000-0003-3039-1076",{"EN":1147},"Robert Muscarella",{"VOID":1149},"A5079291685",{"id":1151,"sortIndex":188,"researcher":24,"roles":1152,"affiliations":1153,"properties":1162,"displayName":1166,"givenName":24,"familyName":24},"6214a2d6-878b-496e-8a1b-160fde832dd1",[],[1154],{"id":1155,"sortIndex":25,"affiliation":1156,"properties":24},"bc6129d7-51e1-485f-a56e-b379d516243c",{"id":1155,"createTime":24,"updateTime":24,"relativeEntities":1157,"slug":24,"properties":1158,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1161,"statistic":24},[],{"title":1159},{"EN":1160},"Department of Biology, City College of the City University of New York, 160 Convent Ave., New York, NY 10031, USA",[],{"orcid":1163,"title":1165,"openalex":1167},{"VOID":1164},"https:\u002F\u002Forcid.org\u002F0000-0002-7025-3551",{"EN":1166},"Peter J. 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Phân tích hình học mô phỏng (geometric morphometrics) thường được sử dụng cho mục đích này, trong đó một tập hợp các biến hình dạng được thu thập từ tọa độ landmark theo một sự chồng chéo \u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Chúng tôi giới thiệu geomorph: một gói phần mềm để thực hiện phân tích hình thái hình học morphometric trong môi trường tính toán thống kê \u003Cjats:sc>r\u003C\u002Fjats:sc>.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Geomorph cung cấp các quy trình cho tất cả các giai đoạn phân tích hình học morphometric dựa trên landmark ở hai và ba chiều. Đây là một gói mã nguồn mở để đọc, thao tác và số hóa dữ liệu landmark, tạo ra các biến hình dạng thông qua phân tích \u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes cho các điểm, đường cong và bề mặt, thực hiện phân tích thống kê về biến thể hình dạng và sự đồng biến, đồng thời cung cấp hình ảnh đồ họa về hình dạng và các mô hình biến thể hình dạng. Một đóng góp quan trọng của geomorph là khả năng thực hiện sự chồng chéo \u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes trên các điểm landmark, cũng như các semilandmarks từ đường cong và bề mặt.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Một loạt các phương pháp thống kê liên quan đến việc kiểm tra các giả thuyết sinh thái và tiến hóa về biến thể hình dạng được cung cấp. Những phương pháp này bao gồm các phương pháp đa biến tiêu chuẩn như phân tích thành phần chính, và các cách tiếp cận cho hồi quy đa biến và so sánh nhóm. Các phương pháp cho các phân tích chuyên biệt hơn, chẳng hạn như đánh giá hình dạng allometry, so sánh các quỹ đạo hình dạng, xem xét sự tích hợp hình thái, và đánh giá tín hiệu phylogenetic, cũng được bao gồm.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Nhiều chức năng được cung cấp để trực quan hóa các kết quả một cách đồ họa, bao gồm các quy trình để xem xét sự biến thiên trong không gian hình dạng, trực quan hóa các quỹ đạo allometric, so sánh các hình dạng cụ thể với nhau và cho việc vẽ các thay đổi phylogenetic trong morphospace.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Cuối cùng, geomorph tham gia vào việc cung cấp các phân tích hình thái hình học morphometric nâng cao thông qua nền tảng tính toán thống kê \u003Cjats:sc>r\u003C\u002Fjats:sc>.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003C\u002Fjats:list>\u003C\u002Fjats:p>","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\u003Cjats:list>\u003Cjats:list-item>\u003Cjats:p>Many ecological and evolutionary studies seek to explain patterns of shape variation and its covariation with other variables. Geometric morphometrics is often used for this purpose, where a set of shape variables are obtained from landmark coordinates following a\u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes superimposition.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>We introduce geomorph: a software package for performing geometric morphometric shape analysis in the\u003Cjats:sc>r\u003C\u002Fjats:sc>statistical computing environment.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Geomorph provides routines for all stages of landmark‐based geometric morphometric analyses in two and three‐dimensions. It is an open source package to read, manipulate, and digitize landmark data, generate shape variables via\u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes analysis for points, curves and surfaces, perform statistical analyses of shape variation and covariation, and to provide graphical depictions of shapes and patterns of shape variation. An important contribution of geomorph is the ability to perform\u003Cjats:styled-content style=\"fixed-case\">P\u003C\u002Fjats:styled-content>rocrustes superimposition on landmark points, as well as semilandmarks from curves and surfaces.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>A wide range of statistical methods germane to testing ecological and evolutionary hypotheses of shape variation are provided. These include standard multivariate methods such as principal components analysis, and approaches for multivariate regression and group comparison. Methods for more specialized analyses, such as for assessing shape allometry, comparing shape trajectories, examining morphological integration, and for assessing phylogenetic signal, are also included.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Several functions are provided to graphically visualize results, including routines for examining variation in shape space, visualizing allometric trajectories, comparing specific shapes to one another and for plotting phylogenetic changes in morphospace.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003Cjats:list-item>\u003Cjats:p>Finally, geomorph participates to make available advanced geometric morphometric analyses through the\u003Cjats:sc>r\u003C\u002Fjats:sc>statistical computing platform.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\u003C\u002Fjats:list>\u003C\u002Fjats:p>",{"EN":1484,"VI":1485},"geomorph: an\u003Cscp>r\u003C\u002Fscp>package for the collection and analysis of geometric morphometric shape data","geomorph: một gói \u003Cscp>r\u003C\u002Fscp> cho việc thu thập và phân tích dữ liệu hình dạng hình học morfometric",{"VI":1124},{"VOID":1488},"10.1111\u002F2041-210x.12035",[169],[171],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002F2041-210X.12035",[1493,1520],{"id":1494,"sortIndex":25,"researcher":24,"roles":1495,"affiliations":1496,"properties":1513,"displayName":1517,"givenName":24,"familyName":24},"4340a4bd-72a5-475c-a3a9-d40707657389",[],[1497,1505],{"id":1498,"sortIndex":25,"affiliation":1499,"properties":24},"17900ef3-efa7-4f10-8741-b4b49f612ee9",{"id":1498,"createTime":24,"updateTime":24,"relativeEntities":1500,"slug":24,"properties":1501,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1504,"statistic":24},[],{"title":1502},{"VI":1503},"Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA",[],{"id":1506,"sortIndex":188,"affiliation":1507,"properties":24},"345f4b0a-5370-4a4a-a7a4-ae717aec3c16",{"id":1506,"createTime":24,"updateTime":24,"relativeEntities":1508,"slug":24,"properties":1509,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1512,"statistic":24},[],{"title":1510},{"VI":1511},"Department of Statistics Iowa State University Ames, IA 50011 USA",[],{"orcid":1514,"title":1516,"openalex":1518},{"VOID":1515},"https:\u002F\u002Forcid.org\u002F0000-0001-9172-7894",{"EN":1517},"Dean C. 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Primer",{},{"id":1745,"createTime":1746,"updateTime":1747,"relativeEntities":1748,"slug":1749,"properties":1750,"entityType":165,"verifyStatus":166,"verifyTime":1746,"verifyNote":167,"languages":1764,"translateLanguages":1765,"viewCount":25,"primaryUrl":1766,"fullTextUrl":24,"authors":1767,"publicationType":240,"publisherRelationship":1806,"citationCount":1859,"citationInfo":1860,"publishDate":1874,"publishYear":1861,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":1875,"openAccess":24,"references":1876,"isForceReanalyzing":474},"a0b43c65-b7b8-4bda-8a61-0a864cfbd648","2024-10-11T23:28:24.917+00:00","2024-12-31T10:05:01.949+00:00",[],"betapart-an-R-package-for-the-study-of-beta-diversity",{"openalex":1751,"mag":1753,"abstract":1755,"title":1758,"keywords":1761,"doi":1762},{"VOID":1752},"W1580156547",{"VOID":1754},"1580156547",{"VI":1756,"EN":1757},"\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>\u003Cjats:bold>1.\u003C\u002Fjats:bold> Đa dạng sinh học beta, tức là sự biến đổi trong thành phần loài giữa các địa điểm, có thể là kết quả của việc thay thế loài giữa các địa điểm (lưu chuyển) và sự mất mát loài giữa các địa điểm (tổn thương lồng ghép).\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>2.\u003C\u002Fjats:bold> Chúng tôi trình bày \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content>, một gói R để tính toán độ khác biệt tổng thể dưới dạng chỉ số Sørensen hoặc Jaccard, cũng như các thành phần lưu chuyển và tổn thương lồng ghép tương ứng của chúng.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>3.\u003C\u002Fjats:bold> \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content> cho phép đánh giá các mẫu không gian của đa dạng sinh học beta sử dụng các biện pháp khác biệt giữa nhiều địa điểm, tính đến sự không đồng nhất trong thành phần giữa vài địa điểm hoặc các biện pháp cặp đôi cung cấp ma trận khoảng cách tính đến cấu trúc đa biến của sự khác biệt.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>4.\u003C\u002Fjats:bold> \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content> cũng cho phép tính toán các mẫu khác biệt theo thời gian trong thành phần quần xã, cùng với các thành phần lưu chuyển và tổn thương lồng ghép của nó.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>5.\u003C\u002Fjats.bold> Nhiều phân tích ví dụ được trình bày, sử dụng dữ liệu có trong gói, để minh họa sự phù hợp của việc phân tách các thành phần lưu chuyển và tổn thương lồng ghép của đa dạng sinh học beta nhằm suy diễn những cơ chế khác nhau đứng sau các mẫu đa dạng sinh học.","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\u003Cjats:bold>1.\u003C\u002Fjats:bold> Beta diversity, that is, the variation in species composition among sites, can be the result of species replacement between sites (turnover) and species loss from site to site (nestedness).\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>2.\u003C\u002Fjats:bold> We present \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content>, an R package for computing total dissimilarity as Sørensen or Jaccard indices, as well as their respective turnover and nestedness components.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>3.\u003C\u002Fjats:bold> \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content> allows the assessment of spatial patterns of beta diversity using multiple‐site dissimilarity measures accounting for compositional heterogeneity across several sites or pairwise measures providing distance matrices accounting for the multivariate structure of dissimilarity.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>4.\u003C\u002Fjats:bold> \u003Cjats:styled-content>betapart\u003C\u002Fjats:styled-content> also allows computing patterns of temporal difference in assemblage composition, and its turnover and nestedness components.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>5.\u003C\u002Fjats:bold> Several example analyses are shown, using the data included in the package, to illustrate the relevance of separating the turnover and nestedness components of beta diversity to infer different mechanisms behind biodiversity patterns.\u003C\u002Fjats:p>",{"EN":1759,"VI":1760},"betapart: an R package for the study of beta diversity","betapart: gói R dùng để nghiên cứu đa dạng sinh học 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Spain",[],{"orcid":1781,"title":1783,"openalex":1785},{"VOID":1782},"https:\u002F\u002Forcid.org\u002F0000-0001-7914-7109",{"EN":1784},"Andrés Baselga",{"VOID":1786},"A5026720975",{"id":1788,"sortIndex":188,"researcher":24,"roles":1789,"affiliations":1790,"properties":1799,"displayName":1803,"givenName":24,"familyName":24},"6b072eb2-c624-4fe8-8b52-3f67978c2773",[],[1791],{"id":1792,"sortIndex":25,"affiliation":1793,"properties":24},"e561326d-77fe-4833-8e02-9585bf94fd28",{"id":1792,"createTime":24,"updateTime":24,"relativeEntities":1794,"slug":24,"properties":1795,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1798,"statistic":24},[],{"title":1796},{"EN":1797},"Division of Biology, Department of Life Sciences, Silwood Park, Ascot, Berkshire SL5 7PY, UK",[],{"orcid":1800,"title":1802,"openalex":1804},{"VOID":1801},"https:\u002F\u002Forcid.org\u002F0000-0002-7005-1394",{"EN":1803},"C. 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R package Version 2.0‐2",{},{"id":24,"text":1923,"url":24,"identifiers":1924},"R Development Core Team, 2011, R: A Language and Environment for Statistical Computing Version 2.13.1",{},{"id":24,"text":1926,"url":24,"identifiers":1927},"10.2475\u002Fajs.241.1.1",{"doi":1926},{"id":24,"text":1929,"url":24,"identifiers":1930},"10.1111\u002Fj.1600-0587.2009.05880.x",{"doi":1929},{"id":24,"text":1932,"url":24,"identifiers":1933},"10.2307\u002F1943563",{"doi":1932},{"id":1935,"createTime":1936,"updateTime":1937,"relativeEntities":1938,"slug":1939,"properties":1940,"entityType":165,"verifyStatus":166,"verifyTime":1954,"verifyNote":167,"languages":1955,"translateLanguages":1956,"viewCount":25,"primaryUrl":1957,"fullTextUrl":24,"authors":1958,"publicationType":240,"publisherRelationship":1978,"citationCount":2031,"citationInfo":2032,"publishDate":2044,"publishYear":297,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":2045,"openAccess":24,"references":2046,"isForceReanalyzing":474},"0c9df121-4e98-4fe8-b1bf-7997c410eec7","2024-08-31T03:13:25.762+00:00","2024-12-31T10:04:05.787+00:00",[],"Simple-means-to-improve-the-interpretability-of-regression-coefficients",{"openalex":1941,"mag":1943,"abstract":1945,"title":1948,"keywords":1951,"doi":1952},{"VOID":1942},"W1609810996",{"VOID":1944},"1609810996",{"VI":1946,"EN":1947},"\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p> \u003Cjats:bold>1.\u003C\u002Fjats:bold> Các mô hình hồi quy tuyến tính là một công cụ thống kê quan trọng trong các nghiên cứu tiến hóa và sinh thái. Thật không may, những mô hình này thường cho ra những ước lượng và kiểm nghiệm giả thuyết không thể giải thích được, đặc biệt là khi các mô hình bao gồm sự tương tác hoặc các hạng tử đa thức. Hơn nữa, các sai số chuẩn cho các nhóm điều trị, mặc dù thường được quan tâm trong việc đưa vào một ấn phẩm, lại không có sẵn trực tiếp trong mô hình hồi quy tuyến tính chuẩn.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>2.\u003C\u002Fjats:bold> Việc trung tâm hóa và chuẩn hóa các biến đầu vào là những phương pháp đơn giản để cải thiện khả năng giải thích của các hệ số hồi quy. Hơn nữa, việc sửa lại mô hình với cấu trúc mô hình hơi thay đổi cho phép rút ra các sai số chuẩn thích hợp cho các nhóm điều trị trực tiếp từ mô hình.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>3.\u003C\u002Fjats:bold> Việc trung tâm hóa sẽ làm cho các hiệu ứng chính có thể giải thích về mặt sinh học ngay cả khi có liên quan đến các sự tương tác, do đó tránh được sự diễn giải sai có thể xảy ra của các hiệu ứng chính. Điều này cũng áp dụng cho việc ước lượng các hiệu ứng tuyến tính trong sự hiện diện của các đa thức. Các biến đầu vào phân loại cũng có thể được trung tâm hóa và điều này đôi khi hỗ trợ cho việc giải thích.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>4.\u003C\u002Fjats.bold> Việc chuẩn hóa (\u003Cjats:italic>z\u003C\u002Fjats:italic>‐biến đổi) các biến đầu vào sẽ dẫn đến việc ước lượng độ dốc chuẩn hóa hoặc các hệ số hồi quy phần chuẩn hóa. Các độ dốc chuẩn hóa có thể so sánh được về độ lớn trong các mô hình cũng như giữa các nghiên cứu. Chúng có một số lợi thế hơn các hệ số tương quan phần và thường là kích thước tác động chuẩn hóa thú vị hơn.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>5.\u003C\u002Fjats:bold> Việc loại bỏ một cách suy nghĩ các giao điểm hoặc hiệu ứng chính cho phép rút ra các trung bình điều trị hoặc độ dốc điều trị và các sai số chuẩn thích hợp của chúng trực tiếp từ một mô hình hồi quy tuyến tính. Điều này cung cấp một lựa chọn đơn giản thay thế cho việc tính sai số chuẩn phức tạp hơn từ các tương phản và các hiệu ứng chính.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>6.\u003C\u002Fjats:bold> Các phương pháp đơn giản được trình bày ở đây tập trung vào ước lượng tham số (ước lượng điểm cũng như khoảng tin cậy) hơn là vào ngưỡng ý nghĩa. Chúng cho phép điều chỉnh các mô hình phức tạp nhưng có nghĩa có thể được trình bày và giải thích một cách ngắn gọn. Các phương pháp được trình bày cũng có thể áp dụng cho các mô hình hồi quy tuyến tính tổng quát (GLM) và các mô hình hồi quy hỗn hợp tuyến tính.","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p> \u003Cjats:bold>1.\u003C\u002Fjats:bold> Linear regression models are an important statistical tool in evolutionary and ecological studies. Unfortunately, these models often yield some uninterpretable estimates and hypothesis tests, especially when models contain interactions or polynomial terms. Furthermore, the standard errors for treatment groups, although often of interest for including in a publication, are not directly available in a standard linear model.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>2.\u003C\u002Fjats:bold> Centring and standardization of input variables are simple means to improve the interpretability of regression coefficients. Further, refitting the model with a slightly modified model structure allows extracting the appropriate standard errors for treatment groups directly from the model.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>3.\u003C\u002Fjats:bold> Centring will make main effects biologically interpretable even when involved in interactions and thus avoids the potential misinterpretation of main effects. This also applies to the estimation of linear effects in the presence of polynomials. Categorical input variables can also be centred and this sometimes assists interpretation.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>4.\u003C\u002Fjats:bold> Standardization (\u003Cjats:italic>z\u003C\u002Fjats:italic>‐transformation) of input variables results in the estimation of standardized slopes or standardized partial regression coefficients. Standardized slopes are comparable in magnitude within models as well as between studies. They have some advantages over partial correlation coefficients and are often the more interesting standardized effect size.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>5.\u003C\u002Fjats:bold> The thoughtful removal of intercepts or main effects allows extracting treatment means or treatment slopes and their appropriate standard errors directly from a linear model. This provides a simple alternative to the more complicated calculation of standard errors from contrasts and main effects.\u003C\u002Fjats:p>\u003Cjats:p> \u003Cjats:bold>6.\u003C\u002Fjats:bold> The simple methods presented here put the focus on parameter estimation (point estimates as well as confidence intervals) rather than on significance thresholds. They allow fitting complex, but meaningful models that can be concisely presented and interpreted. The presented methods can also be applied to generalised linear models (GLM) and linear mixed models.\u003C\u002Fjats:p>",{"EN":1949,"VI":1950},"Simple means to improve the interpretability of regression coefficients","Các phương pháp đơn giản để cải thiện khả năng giải thích của các hệ số hồi 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L.S., 1991, Multiple Regression: Testing and Interpreting Interactions",{},{"id":24,"text":2051,"url":24,"identifiers":2052},"10.1111\u002Fj.1558-5646.1984.tb00344.x",{"doi":2051},{"id":24,"text":2054,"url":24,"identifiers":2055},"10.1037\u002F1082-989X.8.2.129",{"doi":2054},{"id":24,"text":2057,"url":24,"identifiers":2058},"10.3102\u002F10769986031002157",{"doi":2057},{"id":24,"text":2060,"url":24,"identifiers":2061},"10.1016\u002Fj.tree.2008.10.008",{"doi":2060},{"id":24,"text":2063,"url":24,"identifiers":2064},"Bowerman B.L., 1990, Linear Statistical Models: An Appllied 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R",{},{"id":24,"text":2090,"url":24,"identifiers":2091},"10.1093\u002Fbeheco\u002Farp137",{"doi":2090},{"id":24,"text":2093,"url":24,"identifiers":2094},"10.1214\u002F009053604000001048",{"doi":2093},{"id":24,"text":2096,"url":24,"identifiers":2097},"10.1002\u002Fsim.3107",{"doi":2096},{"id":24,"text":2099,"url":24,"identifiers":2100},"Gelman A., 2007, Data Analysis Using Regression and Multilevel\u002FHierarchical Models",{},{"id":24,"text":2102,"url":24,"identifiers":2103},"10.1002\u002Fsim.4780090609",{"doi":2102},{"id":24,"text":2105,"url":24,"identifiers":2106},"10.1207\u002FS15327906MBR3501_1",{"doi":2105},{"id":24,"text":2108,"url":24,"identifiers":2109},"Johnson C.R., 1936, Tests of certain linear hypothesis and their appplication in some educational problems, Statistical Research Memoirs, 1, 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10.1017\u002FCBO9780511605949",{"doi":2144},"10.1017\u002FCBO9780511605949",{"id":24,"text":2146,"url":24,"identifiers":2147},"10.1073\u002Fpnas.94.2.549",{"doi":2146},{"id":24,"text":2149,"url":24,"identifiers":2150},"10.1016\u002Fj.tree.2006.12.003",{"doi":2149},{"id":24,"text":2152,"url":24,"identifiers":2153},"Tabachnick B.G., 2006, Unsing Multivariate Statistics",{},{"id":24,"text":2155,"url":24,"identifiers":2156},"10.1093\u002Fgenetics\u002F3.4.367",{"doi":2155},{"id":24,"text":2158,"url":24,"identifiers":2159},"Zar J.H., 1999, Biostatistical Analysis",{},{"id":2161,"createTime":2162,"updateTime":2163,"relativeEntities":2164,"slug":2165,"properties":2166,"entityType":165,"verifyStatus":166,"verifyTime":2162,"verifyNote":167,"languages":2180,"translateLanguages":2181,"viewCount":25,"primaryUrl":2182,"fullTextUrl":24,"authors":2183,"publicationType":240,"publisherRelationship":2271,"citationCount":2325,"citationInfo":2326,"publishDate":2336,"publishYear":2327,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":2337,"openAccess":24,"references":2338,"isForceReanalyzing":474},"a758161b-7c98-4696-bd79-7278d2dab1c7","2024-08-31T21:53:08.004+00:00","2024-12-31T10:03:07.187+00:00",[],"-scp-ggtree-scp-an-scp-r-scp-package-for-visualization-and-annotation-of-phylogenetic-trees-with-their-covariates-and-other-associated-data",{"openalex":2167,"mag":2169,"abstract":2171,"title":2174,"keywords":2177,"doi":2178},{"VOID":2168},"W2513727910",{"VOID":2170},"2513727910",{"VI":2172,"EN":2173},"\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>Chúng tôi giới thiệu gói \u003Cjats:sc>r\u003C\u002Fjats:sc>, \u003Cjats:sc>ggtree\u003C\u002Fjats:sc>, cung cấp hình ảnh hóa có thể lập trình và chú thích cho các cây phát sinh loài.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>\u003Cjats:sc>ggtree\u003C\u002Fjats:sc> có thể đọc nhiều định dạng tệp cây hơn so với các phần mềm khác, bao gồm các định dạng \u003Cjats:italic>newick\u003C\u002Fjats:italic>, \u003Cjats:italic>nexus\u003C\u002Fjats:italic>, \u003Cjats:italic>NHX\u003C\u002Fjats:italic>, \u003Cjats:italic>phylip\u003C\u002Fjats:italic> và \u003Cjats:italic>jplace\u003C\u002Fjats:italic>, và hỗ trợ hình ảnh hóa các đối tượng cây \u003Cjats:italic>phylo, multiphylo, phylo4, phylo4d, obkdata\u003C\u002Fjats:italic> và \u003Cjats:italic>phyloseq\u003C\u002Fjats:italic> được định nghĩa trong các gói \u003Cjats:sc>r\u003C\u002Fjats:sc> khác. Nó cũng có thể trích xuất các dữ liệu cụ thể về cây\u002Fnhánh\u002Fnút và các dữ liệu khác từ đầu ra phân tích của các phần mềm \u003Cjats:sc>beast\u003C\u002Fjats:sc>, \u003Cjats:sc>epa\u003C\u002Fjats:sc>, \u003Cjats:sc>hyphy\u003C\u002Fjats:sc>, \u003Cjats:sc>paml\u003C\u002Fjats:sc>, \u003Cjats:sc>phylodog\u003C\u002Fjats:sc>, \u003Cjats:sc>pplacer\u003C\u002Fjats:sc>, \u003Cjats:sc>r8s\u003C\u002Fjats:sc>, \u003Cjats:sc>raxml\u003C\u002Fjats:sc> và \u003Cjats:sc>revbayes\u003C\u002Fjats:sc>, và cho phép sử dụng các dữ liệu này để chú thích cây.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Gói này cho phép tô màu và chú thích một cây dựa trên thuộc tính nút số\u002Fnhóm, thao tác một cây bằng cách xoay, thu gọn và phóng to các nhánh, làm nổi bật các nhánh hoặc đơn vị phân loại thuần túy do người dùng chọn và khám phá một cây lớn bằng cách phóng to vào một phần đã chọn.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Một cây hai chiều có thể được vẽ bằng cách điều chỉnh chiều rộng cây dựa trên một thuộc tính của các nút. Một cây có thể được chú thích với một ma trận số liên quan (dưới dạng bản đồ nhiệt), bố trí trình tự đa dạng, đồ thị con hoặc hình ảnh bóng.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Gói \u003Cjats:sc>ggtree\u003C\u002Fjats:sc> được phát hành dưới giấy phép \u003Cjats:sc>artistic-2.0\u003C\u002Fjats:sc>. Mã nguồn và tài liệu của nó có sẵn miễn phí qua \u003Cjats:sc>bioconductor\u003C\u002Fjats:sc> (\u003Cjats:ext-link xmlns:xlink=\"http:\u002F\u002Fwww.w3.org\u002F1999\u002Fxlink\" xlink:href=\"http:\u002F\u002Fwww.bioconductor.org\u002Fpackages\u002Fggtree\">http:\u002F\u002Fwww.bioconductor.org\u002Fpackages\u002Fggtree\u003C\u002Fjats:ext-link>).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>We present an \u003Cjats:sc>r\u003C\u002Fjats:sc> package, \u003Cjats:sc>ggtree\u003C\u002Fjats:sc>, which provides programmable visualization and annotation of phylogenetic trees.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>\u003Cjats:sc>ggtree\u003C\u002Fjats:sc> can read more tree file formats than other softwares, including \u003Cjats:italic>newick\u003C\u002Fjats:italic>,\u003Cjats:italic> nexus\u003C\u002Fjats:italic>,\u003Cjats:italic> NHX\u003C\u002Fjats:italic>,\u003Cjats:italic> phylip\u003C\u002Fjats:italic> and \u003Cjats:italic>jplace\u003C\u002Fjats:italic> formats, and support visualization of \u003Cjats:italic>phylo, multiphylo, phylo4, phylo4d, obkdata\u003C\u002Fjats:italic> and \u003Cjats:italic>phyloseq\u003C\u002Fjats:italic> tree objects defined in other \u003Cjats:sc>r\u003C\u002Fjats:sc> packages. It can also extract the tree\u002Fbranch\u002Fnode‐specific and other data from the analysis outputs of \u003Cjats:sc>beast\u003C\u002Fjats:sc>,\u003Cjats:sc> epa\u003C\u002Fjats:sc>,\u003Cjats:sc> hyphy\u003C\u002Fjats:sc>,\u003Cjats:sc> paml\u003C\u002Fjats:sc>,\u003Cjats:sc> phylodog\u003C\u002Fjats:sc>,\u003Cjats:sc> pplacer\u003C\u002Fjats:sc>,\u003Cjats:sc> r8s\u003C\u002Fjats:sc>,\u003Cjats:sc> raxml\u003C\u002Fjats:sc> and \u003Cjats:sc>revbayes\u003C\u002Fjats:sc> software, and allows using these data to annotate the tree.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>The package allows colouring and annotation of a tree by numerical\u002Fcategorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. 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The source code and documents are freely available through \u003Cjats:sc>bioconductor\u003C\u002Fjats:sc> (\u003Cjats:ext-link xmlns:xlink=\"http:\u002F\u002Fwww.w3.org\u002F1999\u002Fxlink\" xlink:href=\"http:\u002F\u002Fwww.bioconductor.org\u002Fpackages\u002Fggtree\">http:\u002F\u002Fwww.bioconductor.org\u002Fpackages\u002Fggtree\u003C\u002Fjats:ext-link>).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>",{"EN":2175,"VI":2176},"\u003Cscp>ggtree\u003C\u002Fscp>: an \u003Cscp>r\u003C\u002Fscp> package for visualization and annotation of phylogenetic trees with their covariates and other associated data","\u003Cscp>ggtree\u003C\u002Fscp>: một gói \u003Cscp>r\u003C\u002Fscp> để trực quan hóa và chú thích các cây phát sinh loài cùng với các biến liên quan và dữ liệu khác",{"VI":1124},{"VOID":2179},"10.1111\u002F2041-210x.12628",[169],[171],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002F2041-210X.12628",[2184,2203,2220,2237,2254],{"id":2185,"sortIndex":25,"researcher":24,"roles":2186,"affiliations":2187,"properties":2196,"displayName":2200,"givenName":24,"familyName":24},"c18a7509-8948-42b2-8895-3832713a4f21",[],[2188],{"id":2189,"sortIndex":25,"affiliation":2190,"properties":24},"b0b206dd-b2f2-4a77-a24c-6f7d3e5fb706",{"id":2189,"createTime":24,"updateTime":24,"relativeEntities":2191,"slug":24,"properties":2192,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2195,"statistic":24},[],{"title":2193},{"EN":2194},"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China",[],{"orcid":2197,"title":2199,"openalex":2201},{"VOID":2198},"https:\u002F\u002Forcid.org\u002F0000-0002-6485-8781",{"EN":2200},"Guangchuang Yu",{"VOID":2202},"A5027320896",{"id":2204,"sortIndex":188,"researcher":24,"roles":2205,"affiliations":2206,"properties":2213,"displayName":2217,"givenName":24,"familyName":24},"d78adb07-f4fb-45a1-ad28-e2304c642494",[],[2207],{"id":2189,"sortIndex":25,"affiliation":2208,"properties":24},{"id":2189,"createTime":24,"updateTime":24,"relativeEntities":2209,"slug":24,"properties":2210,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2212,"statistic":24},[],{"title":2211},{"EN":2194},[],{"orcid":2214,"title":2216,"openalex":2218},{"VOID":2215},"https:\u002F\u002Forcid.org\u002F0000-0003-3608-0586",{"EN":2217},"David K. 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Available at:http:\u002F\u002Ftree.bio.ed.ac.uk\u002Fsoftware\u002Ffigtree\u002F(accessed 10 March 2015).",{},{"id":24,"text":2403,"url":24,"identifiers":2404},"10.1111\u002Fj.2041-210X.2011.00169.x",{"doi":2403},{"id":24,"text":2406,"url":24,"identifiers":2407},"10.1002\u002Fjez.b.19",{"doi":2406},{"id":24,"text":2409,"url":24,"identifiers":2410},"10.1093\u002Fsysbio\u002Fsyu039",{"doi":2409},{"id":24,"text":2412,"url":24,"identifiers":2413},"10.1093\u002Fbioinformatics\u002Fbtu033",{"doi":2412},{"id":24,"text":2415,"url":24,"identifiers":2416},"10.1007\u002F978-0-387-98141-3",{"doi":2415},{"id":24,"text":2418,"url":24,"identifiers":2419},"Wilkinson L., 2005, The Grammar of Graphics",{},{"id":24,"text":2421,"url":24,"identifiers":2422},"10.1093\u002Fmolbev\u002Fmsm088",{"doi":2421},{"id":24,"text":2424,"url":24,"identifiers":2425},"Yu G., 2016, Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution",{},{"id":24,"text":2427,"url":24,"identifiers":2428},"10.1093\u002Fnar\u002Fgks576",{"doi":2427},{"id":2430,"createTime":2431,"updateTime":2432,"relativeEntities":2433,"slug":2434,"properties":2435,"entityType":165,"verifyStatus":23,"verifyTime":2431,"verifyNote":2449,"languages":2450,"translateLanguages":2451,"viewCount":25,"primaryUrl":2452,"fullTextUrl":24,"authors":2453,"publicationType":240,"publisherRelationship":2465,"citationCount":2518,"citationInfo":2519,"publishDate":2532,"publishYear":1861,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":2533,"openAccess":24,"references":2534,"isForceReanalyzing":474},"49f9cdcc-0c70-4d5e-b495-1027b334c6e1","2024-09-02T21:12:53.933+00:00","2024-12-31T10:02:08.412+00:00",[],"phytools-an-R-package-for-phylogenetic-comparative-biology-and-other-things-",{"openalex":2436,"mag":2438,"abstract":2440,"title":2443,"keywords":2446,"doi":2447},{"VOID":2437},"W1605984840",{"VOID":2439},"1605984840",{"VI":2441,"EN":2442},"\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>\u003Cjats:bold>1.\u003C\u002Fjats:bold> Tại đây, tôi trình bày một gói phần mềm phát sinh chủng loài đa chức năng mới, phytools, dành cho môi trường tính toán thống kê R.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>2.\u003C\u002Fjats:bold> Trọng tâm của gói này là các phương pháp cho sinh học so sánh phát sinh chủng loài; tuy nhiên, nó cũng bao gồm các công cụ cho việc suy diễn cây, nhập\u002Fxuất phát sinh chủng loài, vẽ đồ thị, thao tác và một số nhiệm vụ khác.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats.bold>3.\u003C\u002Fjats.bold> Tôi mô tả và lập bảng các phương pháp chính được triển khai trong phytools, và bên cạnh đó cung cấp một số minh họa về cách sử dụng nó dưới dạng hai ví dụ tiêu biểu.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>4.\u003C\u002Fjats.bold> Cuối cùng, tôi kết luận bằng cách mô tả ngắn gọn một blog trực tuyến mà tôi sử dụng để tài liệu hóa các phát triển hiện tại và tương lai cho phytools. Tôi cũng lưu ý các tài nguyên web khác dành cho phát sinh chủng loài trong môi trường tính toán R.","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\u003Cjats:bold>1.\u003C\u002Fjats:bold> Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>2.\u003C\u002Fjats:bold> The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input\u002Foutput, plotting, manipulation and several other tasks.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>3.\u003C\u002Fjats:bold> I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.\u003C\u002Fjats:p>\u003Cjats:p>\u003Cjats:bold>4.\u003C\u002Fjats:bold> Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. 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Các tiêu chí thông tin, chẳng hạn như Tiêu chí Thông tin Akaike (\u003Cjats:styled-content style=\"fixed-case\">AIC\u003C\u002Fjats:styled-content>), thường được trình bày như các công cụ so sánh mô hình cho các mô hình hỗn hợp.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Tuy nhiên, việc trình bày ‘phương sai giải thích’ (\u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup>) như một thống kê tóm tắt có liên quan của các mô hình hỗn hợp là điều hiếm gặp, mặc dù \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> thường được báo cáo cho các mô hình tuyến tính (\u003Cjats:styled-content style=\"fixed-case\">LM\u003C\u002Fjats:styled-content>s) và cả các mô hình tuyến tính tổng quát (\u003Cjats:styled-content style=\"fixed-case\">GLM\u003C\u002Fjats:styled-content>s). \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> có đặc tính cực kỳ hữu ích là cung cấp giá trị tuyệt đối cho độ khớp của một mô hình, điều mà các tiêu chí thông tin không thể cung cấp. Như một thống kê tóm tắt mô tả lượng phương sai được giải thích, \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cũng có thể là một đại lượng có ý nghĩa sinh học.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Một lý do cho việc thiếu appreciation đối với \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> trong các mô hình hỗn hợp nằm ở thực tế rằng \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> có thể được định nghĩa theo nhiều cách khác nhau. Hơn nữa, hầu hết các định nghĩa của \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cho các mô hình hỗn hợp có các vấn đề lý thuyết (ví dụ: giá trị \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> giảm hoặc âm trong các mô hình lớn hơn) và\u002Fhoặc việc sử dụng chúng gặp khó khăn với các vấn đề thực tiễn (ví dụ: việc thực hiện).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Tại đây, chúng tôi đề xuất tầm quan trọng của việc báo cáo \u003Cjats:italic>R\u003C\u002Fjats italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cho các mô hình hỗn hợp. Chúng tôi đầu tiên cung cấp các định nghĩa phổ biến của \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cho \u003Cjats:styled-content style=\"fixed-case\">LM\u003C\u002Fjats:styled-content>s và \u003Cjats:styled-content style=\"fixed-case\">GLM\u003C\u002Fjats:styled-content>s và thảo luận về các vấn đề chính liên quan đến việc tính toán \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cho các mô hình hỗn hợp. Sau đó, chúng tôi khuyến nghị một phương pháp tổng quát và đơn giản để tính toán hai loại \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> (marginal và conditional \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup>) cho cả \u003Cjats:styled-content style=\"fixed-case\">LMM\u003C\u002Fjats:styled-content>s và \u003Cjats:styled-content style=\"fixed-case\">GLMM\u003C\u002Fjats:styled-content>s, ít bị ảnh hưởng bởi các vấn đề thường gặp.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Phương pháp này được minh họa qua các ví dụ và có thể được sử dụng rộng rãi bởi các nhà nghiên cứu trong mọi lĩnh vực nghiên cứu, bất kể gói phần mềm nào được sử dụng để phù hợp với các mô hình hỗn hợp. Phương pháp được đề xuất có khả năng tạo điều kiện cho việc trình bày \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> cho nhiều hoàn cảnh khác nhau.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>","\u003Cjats:title>Summary\u003C\u002Fjats:title>\u003Cjats:p>\n\u003Cjats:list>\n\n\u003Cjats:list-item>\u003Cjats:p>The use of both linear and generalized linear mixed‐effects models (\u003Cjats:styled-content style=\"fixed-case\">LMM\u003C\u002Fjats:styled-content>s and \u003Cjats:styled-content style=\"fixed-case\">GLMM\u003C\u002Fjats:styled-content>s) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion (\u003Cjats:styled-content style=\"fixed-case\">AIC\u003C\u002Fjats:styled-content>), are usually presented as model comparison tools for mixed‐effects models.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>The presentation of ‘variance explained’ (\u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup>) as a relevant summarizing statistic of mixed‐effects models, however, is rare, even though \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> is routinely reported for linear models (\u003Cjats:styled-content style=\"fixed-case\">LM\u003C\u002Fjats:styled-content>s) and also generalized linear models (\u003Cjats:styled-content style=\"fixed-case\">GLM\u003C\u002Fjats:styled-content>s). \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> has the extremely useful property of providing an absolute value for the goodness‐of‐fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> can also be a quantity of biological interest.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>One reason for the under‐appreciation of \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for mixed‐effects models lies in the fact that \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> can be defined in a number of ways. Furthermore, most definitions of \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for mixed‐effects have theoretical problems (e.g. decreased or negative \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> values in larger models) and\u002For their use is hindered by practical difficulties (e.g. implementation).\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>Here, we make a case for the importance of reporting \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for mixed‐effects models. We first provide the common definitions of \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for \u003Cjats:styled-content style=\"fixed-case\">LM\u003C\u002Fjats:styled-content>s and \u003Cjats:styled-content style=\"fixed-case\">GLM\u003C\u002Fjats:styled-content>s and discuss the key problems associated with calculating \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for mixed‐effects models. We then recommend a general and simple method for calculating two types of \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> (marginal and conditional \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup>) for both \u003Cjats:styled-content style=\"fixed-case\">LMM\u003C\u002Fjats:styled-content>s and \u003Cjats:styled-content style=\"fixed-case\">GLMM\u003C\u002Fjats:styled-content>s, which are less susceptible to common problems.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\n\u003Cjats:list-item>\u003Cjats:p>This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed‐effects models. The proposed method has the potential to facilitate the presentation of \u003Cjats:italic>R\u003C\u002Fjats:italic>\u003Cjats:sup>2\u003C\u002Fjats:sup> for a wide range of circumstances.\u003C\u002Fjats:p>\u003C\u002Fjats:list-item>\n\u003C\u002Fjats:list>\n\u003C\u002Fjats:p>",{"EN":2684,"VI":2685},"A general and simple method for obtaining \u003Ci>R\u003C\u002Fi>\u003Csup>2\u003C\u002Fsup> from generalized linear mixed‐effects models","Một phương pháp tổng quát và đơn giản để tính toán \u003Ci>R\u003C\u002Fi>\u003Csup>2\u003C\u002Fsup> từ các mô hình hỗn hợp tuyến tính tổng quát",{"VI":2687},"mô hình hỗn hợp, R2, phân tích thống kê, sinh học, sinh thái học",{"VOID":2689},"10.1111\u002Fj.2041-210x.2012.00261.x",[169],[171],"https:\u002F\u002Fbesjournals.onlinelibrary.wiley.com\u002Fdoi\u002F10.1111\u002Fj.2041-210x.2012.00261.x",[2694,2721],{"id":2695,"sortIndex":25,"researcher":24,"roles":2696,"affiliations":2697,"properties":2714,"displayName":2718,"givenName":24,"familyName":24},"22a2b628-208c-439f-9e6a-468990c95748",[],[2698,2706],{"id":2699,"sortIndex":25,"affiliation":2700,"properties":24},"2763b72b-df41-49d9-b4c5-9a44038a88e9",{"id":2699,"createTime":24,"updateTime":24,"relativeEntities":2701,"slug":24,"properties":2702,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2705,"statistic":24},[],{"title":2703},{"EN":2704},"Department of Behavioral Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Eberhard‐Gwinner‐Straße, 82319 Seewiesen Germany",[],{"id":2707,"sortIndex":188,"affiliation":2708,"properties":24},"b273016b-763d-42c0-a7b1-8a2f697b66b4",{"id":2707,"createTime":24,"updateTime":24,"relativeEntities":2709,"slug":24,"properties":2710,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2713,"statistic":24},[],{"title":2711},{"EN":2712},"National Centre for Growth and Development, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand",[],{"orcid":2715,"title":2717,"openalex":2719},{"VOID":2716},"https:\u002F\u002Forcid.org\u002F0000-0002-7765-5182",{"EN":2718},"Shinichi 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Germany",[],{"orcid":2734,"title":2735,"openalex":2736},{"VOID":1973},{"EN":1975},{"VOID":1977},{"url":24,"publisher":2738,"properties":2785},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":2739,"slug":10,"properties":2740,"entityType":22,"verifyStatus":23,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":25,"subjectFields":2745,"manageAffiliations":2754,"indexDatabases":2765,"url":90,"thumbnailPath":24,"statistic":2780,"gsStatistic":24,"type":24,"analyzePriority":24},[],{"country":2741,"eissn":2742,"issn":2743,"title":2744},{"VOID":13},{"VOID":15},{"VOID":17},{"EN":19},[2746,2750],{"id":28,"createTime":24,"updateTime":24,"relativeEntities":2747,"label":2748,"description":2749,"parentId":24,"standard":24,"scholarHubFieldId":24},[],{"EN":31},{},{"id":34,"createTime":24,"updateTime":24,"relativeEntities":2751,"label":2752,"description":2753,"parentId":24,"standard":24,"scholarHubFieldId":24},[],{"EN":37},{},[2755,2760],{"id":41,"createTime":24,"updateTime":24,"relativeEntities":2756,"slug":24,"properties":2757,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2759,"statistic":24},[],{"title":2758},{"EN":45},[],{"id":48,"createTime":24,"updateTime":24,"relativeEntities":2761,"slug":24,"properties":2762,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2764,"statistic":24},[],{"title":2763},{"EN":52},[],[2766,2773],{"id":56,"indexDatabase":2767,"url":69,"indexYears":24,"academicFieldIds":2772,"indexDatabaseRanking":24},{"id":58,"createTime":24,"updateTime":24,"relativeEntities":2768,"label":2769,"description":2770,"key":65,"publicationTags":2771,"standard":24},[],{"EN":61,"VI":61},{"EN":63,"VI":64},[67,68],[71],{"id":73,"indexDatabase":2774,"url":84,"indexYears":85,"academicFieldIds":2779,"indexDatabaseRanking":89},{"id":75,"createTime":24,"updateTime":24,"relativeEntities":2775,"label":2776,"description":2777,"key":81,"publicationTags":2778,"standard":24},[],{"EN":78,"VI":78},{"EN":78,"VI":80},[83],[87,88],{"impactFactor":25,"impactFactorByYear":2781,"i10Index":105,"i10IndexLast5Year":106,"totalPublication":107,"totalPublicationByYear":2782,"totalCitation":117,"totalCitationByYear":2783,"totalCitationPerPublication":131,"totalCitationPerPublicationByYear":2784,"hindexLast5Year":93,"hindex":93},{"2012":93,"2013":94,"2014":95,"2015":96,"2016":97,"2017":98,"2018":99,"2019":100,"2020":101,"2021":102,"2022":103,"2023":104},{"2010":109,"2011":109,"2012":110,"2013":111,"2014":112,"2015":112,"2016":109,"2017":113,"2018":114,"2019":115,"2020":116,"2021":109},{"2010":119,"2011":120,"2012":121,"2013":122,"2014":123,"2015":124,"2016":125,"2017":126,"2018":127,"2019":128,"2020":129,"2021":130},{"2010":133,"2011":134,"2012":135,"2013":136,"2014":137,"2015":138,"2016":139,"2017":140,"2018":141,"2019":142,"2020":143,"2021":144},{"issue":2786,"pages":2787,"volume":2789},{"VOID":1001},{"VOID":2788},"133-142",{"VOID":1595},8156,{"total":2790,"publishYear":1601,"statisticByYear":2792},{"2012":188,"2013":1603,"2014":2793,"2015":2794,"2016":2795,"2017":2796,"2018":2797,"2019":2798,"2020":2799,"2021":2800,"2022":2801,"2023":2802,"2024":2803},234,437,576,773,900,935,962,1016,838,785,441,"2013-02-01",[67,89],[2807,2810,2813,2815,2818,2820,2823,2826,2829,2832,2835,2837,2840,2842,2845,2848,2851,2854,2857,2860,2863,2866,2869,2872,2875,2878,2881,2883,2886,2889,2891,2893,2896,2899,2902,2904,2907,2910,2913,2916,2919,2922,2925,2928],{"id":24,"text":2808,"url":24,"identifiers":2809},"Akaike H., 1973, 2nd International Symposium on Information Theory, 267",{},{"id":24,"text":2811,"url":24,"identifiers":2812},"Bates D. Maechler M.&Bolker B.(2011)lme4: linear mixed‐effects models. R package version 0.999375‐42.http:\u002F\u002FCRAN.R-project.org\u002Fpackage=lme4.",{},{"id":24,"text":2060,"url":24,"identifiers":2814},{"doi":2060},{"id":24,"text":2816,"url":24,"identifiers":2817},"Bryk A.S., 1992, Hierarchical Linear Models",{},{"id":24,"text":2078,"url":24,"identifiers":2819},{},{"id":24,"text":2821,"url":24,"identifiers":2822},"Cameron A.C., 1996, R‐squared measures for count data regression models with applications to health‐care utilization, Journal of Business & Economic Statistics, 14, 209",{},{"id":24,"text":2824,"url":24,"identifiers":2825},"10.1016\u002FS0304-4076(96)01818-0",{"doi":2824},{"id":24,"text":2827,"url":24,"identifiers":2828},"Claeskens G., 2009, Model Selection and Model Averaging",{},{"id":24,"text":2830,"url":24,"identifiers":2831},"10.1201\u002F9781584887218",{"doi":2830},{"id":24,"text":2833,"url":24,"identifiers":2834},"10.1086\u002F661244",{"doi":2833},{"id":24,"text":343,"url":24,"identifiers":2836},{"doi":343},{"id":24,"text":2838,"url":24,"identifiers":2839},"10.1002\u002Fsim.3429",{"doi":2838},{"id":24,"text":2099,"url":24,"identifiers":2841},{},{"id":24,"text":2843,"url":24,"identifiers":2844},"10.1198\u002F004017005000000517",{"doi":2843},{"id":24,"text":2846,"url":24,"identifiers":2847},"10.1207\u002FS15328031US0104_02",{"doi":2846},{"id":24,"text":2849,"url":24,"identifiers":2850},"10.1111\u002Fj.1420-9101.2010.02210.x",{"doi":2849},{"id":24,"text":2852,"url":24,"identifiers":2853},"10.18637\u002Fjss.v033.i02",{"doi":2852},{"id":24,"text":2855,"url":24,"identifiers":2856},"Hamaker E.L., 2011, Handbook of Advanced Multilevel Analysis, 231",{},{"id":24,"text":2858,"url":24,"identifiers":2859},"10.1016\u002Fj.jspi.2007.11.010",{"doi":2858},{"id":24,"text":2861,"url":24,"identifiers":2862},"10.2307\u002F2683704",{"doi":2861},{"id":24,"text":2864,"url":24,"identifiers":2865},"10.1080\u002F02664760802124422",{"doi":2864},{"id":24,"text":2867,"url":24,"identifiers":2868},"10.1017\u002FCBO9780511810176",{"doi":2867},{"id":24,"text":2870,"url":24,"identifiers":2871},"10.2307\u002F2685605",{"doi":2870},{"id":24,"text":2873,"url":24,"identifiers":2874},"10.1136\u002Fjech.2004.028035",{"doi":2873},{"id":24,"text":2876,"url":24,"identifiers":2877},"10.1136\u002Fjech.2004.023929",{"doi":2876},{"id":24,"text":2879,"url":24,"identifiers":2880},"10.1093\u002Fbiomet\u002F78.3.691",{"doi":2879},{"id":24,"text":2117,"url":24,"identifiers":2882},{"doi":2117},{"id":24,"text":2884,"url":24,"identifiers":2885},"10.1111\u002Fj.1469-185X.2010.00141.x",{"doi":2884},{"id":24,"text":2887,"url":24,"identifiers":2888},"10.1016\u002Fj.csda.2007.06.006",{"doi":2887},{"id":24,"text":419,"url":24,"identifiers":2890},{"doi":419},{"id":24,"text":1715,"url":24,"identifiers":2892},{},{"id":24,"text":2894,"url":24,"identifiers":2895},"10.2307\u002F2112482",{"doi":2894},{"id":24,"text":2897,"url":24,"identifiers":2898},"Roberts J.K., 2011, Handbook of Advanced Multilevel Analysis, 219",{},{"id":24,"text":2900,"url":24,"identifiers":2901},"10.1111\u002Fj.2041-210X.2010.00012.x",{"doi":2900},{"id":24,"text":2139,"url":24,"identifiers":2903},{"doi":2139},{"id":24,"text":2905,"url":24,"identifiers":2906},"Schielzeth H., 2012, Nested by design: model fitting and interpretation in a mixed model era, Methods in Ecology and Evolution",{},{"id":24,"text":2908,"url":24,"identifiers":2909},"10.1214\u002Faos\u002F1176344136",{"doi":2908},{"id":24,"text":2911,"url":24,"identifiers":2912},"10.1177\u002F0049124194022003004",{"doi":2911},{"id":24,"text":2914,"url":24,"identifiers":2915},"Snijders T., 1999, Multilevel Analysis: An Introduction to Basic and Advanced Multilevel Modeling",{},{"id":24,"text":2917,"url":24,"identifiers":2918},"10.1007\u002F978-3-642-04898-2_387",{"doi":2917},{"id":24,"text":2920,"url":24,"identifiers":2921},"10.1111\u002F1467-9868.00353",{"doi":2920},{"id":24,"text":2923,"url":24,"identifiers":2924},"10.1198\u002Ftast.2009.08210",{"doi":2923},{"id":24,"text":2926,"url":24,"identifiers":2927},"10.2307\u002F2532896",{"doi":2926},{"id":24,"text":2929,"url":24,"identifiers":2930},"10.1002\u002Fsim.1572",{"doi":2929}]