{ "_id": "6a1f1072b401979e7341d7b5", "Package": "DImodels", "Type": "Package", "Title": "Diversity-Interactions (DI) Models", "Version": "1.3.3", "Date": "2025-07-24", "Authors@R": "c(person(\"Rafael\", \"de Andrade Moral\", role = c(\"aut\", \"cre\"), email = \"rafael.deandrademoral@mu.ie\"), person(\"John\", \"Connolly\", role = \"aut\"), person(\"Rishabh\", \"Vishwakarma\", role = \"ctb\"), person(\"Caroline\", \"Brophy\", role = \"aut\"))", "Author": "Rafael de Andrade Moral [aut, cre], John Connolly [aut],\nRishabh Vishwakarma [ctb], Caroline Brophy [aut]", "Maintainer": "Rafael de Andrade Moral ", "URL": "https://dimodels.com/, https://github.com/rafamoral/DImodels", "BugReports": "https://github.com/rafamoral/DImodels/issues", "VignetteBuilder": "knitr", "Description": "The 'DImodels' package is suitable for analysing data from\nbiodiversity and ecosystem function studies using the\nDiversity-Interactions (DI) modelling approach introduced by\nKirwan et al. (2009) . Suitable data\nwill contain proportions for each species and a community-level\nresponse variable, and may also include additional factors,\nsuch as blocks or treatments. The package can perform data\nmanipulation tasks, such as computing pairwise interactions\n(the DI_data() function), can perform an automated model\nselection process (the autoDI() function) and has the\nflexibility to fit a wide range of user-defined DI models (the\nDI() function).", "License": "GPL (>=2)", "NeedsCompilation": "no", "Config/testthat/edition": "3", "RoxygenNote": "7.3.2", "Repository": "https://rafamoral.r-universe.dev", "Date/Publication": "2025-08-05 08:05:04 UTC", "RemoteUrl": "https://github.com/rafamoral/dimodels", "RemoteRef": "HEAD", "RemoteSha": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "Packaged": { "Date": "2026-05-17 08:16:31 UTC", "User": "root" }, "MD5sum": "b394c6451bef3aa840a14ea98ed87396", "_user": "rafamoral", "_type": "src", "_file": "DImodels_1.3.3.tar.gz", "_fileid": "ebe95519d081c5fe7d1d10ccb10561c8286d7c00cd5293212b7f2955626ae6bb", "_filesize": 666427, "_sha256": "ebe95519d081c5fe7d1d10ccb10561c8286d7c00cd5293212b7f2955626ae6bb", "_created": "2026-05-17T08:16:31.000Z", "_published": "2026-06-02T17:18:42.337Z", "_distro": "noble", "_jobs": [ { "job": 79130141648, "time": 186, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7040756987" }, { "job": 79130142033, "time": 182, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7040756553" }, { "job": 79130141677, "time": 171, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7040753330" }, { "job": 79130141772, "time": 172, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7040752756" }, { "job": 79130141611, "time": 186, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7040736002" }, { "job": 79130141341, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7364887178" }, { "job": 79130141672, "time": 150, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7040753411" }, { "job": 79130141769, "time": 152, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7040753303" }, { "job": 79130142027, "time": 150, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7040753065" } ], "_buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rafamoral/dimodels", "_commit": { "id": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "author": "Rishabh Vishwakarma ", "committer": "Rishabh Vishwakarma ", "message": "DImodels v1.3.3 release\n", "time": 1754381104 }, "_maintainer": { "name": "Rafael de Andrade Moral", "email": "rafael.deandrademoral@mu.ie" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "hnp", "role": "Imports" }, { "package": "rootSolve", "role": "Imports" }, { "package": "multcomp", "role": "Imports" }, { "package": "multcompView", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "rafamoral", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2025-30", "n": 2 }, { "week": "2025-32", "n": 2 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "rishvish", "count": 17, "uuid": 39990848 }, { "user": "rafamoral", "count": 1, "uuid": 10039600 } ], "_userbio": { "uuid": 10039600, "type": "user", "name": "Rafael de Andrade Moral", "description": "Associate Professor of Statistics, researching statistical methods applied to Ecology, Biology and Agriculture." }, "_downloads": { "count": 276, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DImodels" }, "_devurl": "https://github.com/rafamoral/dimodels", "_searchresults": 114, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DImodels.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rafamoral/dimodels", "_realowner": "rafamoral", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2020-10-01" }, { "version": "1.1", "date": "2021-06-25" }, { "version": "1.2", "date": "2022-11-25" }, { "version": "1.2.1", "date": "2023-05-22" }, { "version": "1.3", "date": "2023-11-22" }, { "version": "1.3.1", "date": "2024-01-24" }, { "version": "1.3.2", "date": "2024-02-28" }, { "version": "1.3.3", "date": "2025-08-19" } ], "_exports": [ "autoDI", "compare_communities", "contrast_matrix", "contrasts_DI", "describe_model", "DI", "DI_compare", "DI_data", "DI_data_ADD", "DI_data_E_AV", "DI_data_FG", "DI_data_fullpairwise", "DI_data_prepare", "extract", "richness_vs_DI", "theta_CI", "update_DI" ], "_datasets": [ { "name": "Bell", "title": "The \"Bell\" Dataset", "object": "Bell", "file": "Bell.rda", "class": [ "data.frame" ], "fields": [ "id", "community", "richness", "p1", "p2", "p3", "p4", "p5", "p6", "p7", "p8", "p9", "p10", "p11", "p12", "p13", "p14", "p15", "p16", "p17", "p18", "p19", "p20", "p21", "p22", "p23", "p24", "p25", "p26", "p27", "p28", "p29", "p30", "p31", "p32", "p33", "p34", "p35", "p36", "p37", "p38", "p39", "p40", "p41", "p42", "p43", "p44", "p45", "p46", "p47", "p48", "p49", "p50", "p51", "p52", "p53", "p54", "p55", "p56", "p57", "p58", "p59", "p60", "p61", "p62", "p63", "p64", "p65", "p66", "p67", "p68", "p69", "p70", "p71", "p72", "response" ], "rows": 1374, "table": true, "tojson": true }, { "name": "design_a", "title": "The \"design_a\" Dataset", "object": "design_a", "file": "design_a.rda", "class": [ "data.frame" ], "fields": [ "community", "richness", "p1", "p2", "p3", "p4", "p5", "p6", "p7", "p8", "p9" ], "rows": 206, "table": true, "tojson": true }, { "name": "design_b", "title": "The \"design_b\" Dataset", "object": "design_b", "file": "design_b.rda", "class": [ "data.frame" ], "fields": [ "richness", "p1", "p2", "p3", "p4", "p5", "p6" ], "rows": 47, "table": true, "tojson": true }, { "name": "sim0", "title": "The Simulated \"sim0\" Dataset", "object": "sim0", "file": "sim0.rda", "class": [ "data.frame" ], "fields": [ "community", "richness", "p1", "p2", "p3", "response" ], "rows": 64, "table": true, "tojson": true }, { "name": "sim0_design", "title": "The \"sim0_design\" Dataset", "object": "sim0_design", "file": "sim0_design.rda", "class": [ "data.frame" ], "fields": [ "community", "richness", "p1", "p2", "p3" ], "rows": 16, "table": true, "tojson": true }, { "name": "sim1", "title": "The Simulated \"sim1\" Dataset", "object": "sim1", "file": "sim1.rda", "class": [ "data.frame" ], "fields": [ "community", "block", "p1", "p2", "p3", "p4", "response" ], "rows": 60, "table": true, "tojson": true }, { "name": "sim2", "title": "The Simulated \"sim2\" Dataset", "object": "sim2", "file": "sim2.rda", "class": [ "data.frame" ], "fields": [ "community", "block", "p1", "p2", "p3", "p4", "response" ], "rows": 60, "table": true, "tojson": true }, { "name": "sim3", "title": "The Simulated \"sim3\" Dataset", "object": "sim3", "file": "sim3.rda", "class": [ "data.frame" ], "fields": [ "community", "richness", "treatment", "p1", "p2", "p3", "p4", "p5", "p6", "p7", "p8", "p9", "response" ], "rows": 412, "table": true, "tojson": true }, { "name": "sim4", "title": "The Simulated \"sim4\" Dataset", "object": "sim4", "file": "sim4.rda", "class": [ "data.frame" ], "fields": [ "richness", "treatment", "p1", "p2", "p3", "p4", "p5", "p6", "response" ], "rows": 141, "table": true, "tojson": true }, { "name": "sim5", "title": "The Simulated \"sim5\" Dataset", "object": "sim5", "file": "sim5.rda", "class": [ "data.frame" ], "fields": [ "community", "richness", "p1", "p2", "p3", "p4", "p5", "p6", "p7", "p8", "p9", "response" ], "rows": 206, "table": true, "tojson": true }, { "name": "Switzerland", "title": "The \"Switzerland\" Dataset", "object": "Switzerland", "file": "Switzerland.rda", "class": [ "data.frame" ], "fields": [ "plot", "nitrogen", "density", "p1", "p2", "p3", "p4", "yield" ], "rows": 68, "table": true, "tojson": true } ], "_help": [ { "page": "DImodels-package", "title": "Diversity-Interactions (DI) Models", "topics": [ "DImodels-package", "DImodels" ] }, { "page": "autoDI", "title": "Automated Diversity-Interactions Model Fitting", "topics": [ "autoDI" ] }, { "page": "Bell", "title": "The \"Bell\" Dataset", "topics": [ "Bell" ] }, { "page": "compare_communities", "title": "Compare communities and assign compact letter displays (CLD)", "topics": [ "compare_communities" ] }, { "page": "contrasts_DI", "title": "Compute contrasts for Diversity Interactions (DI) models", "topics": [ "contrasts_DI", "contrast_matrix" ] }, { "page": "describe_model", "title": "Describe DI models", "topics": [ "describe_model" ] }, { "page": "design_a", "title": "The \"design_a\" Dataset", "topics": [ "design_a" ] }, { "page": "design_b", "title": "The \"design_b\" Dataset", "topics": [ "design_b" ] }, { "page": "DI", "title": "Diversity-Interactions Model Fitting", "topics": [ "DI", "DI_ADD", "DI_ADD_treat", "DI_AV", "DI_AV_treat", "DI_CUSTOM", "DI_E", "DI_E_treat", "DI_FG", "DI_FG_treat", "DI_FULL", "DI_FULL_treat", "DI_ID", "DI_ID_treat", "DI_STR", "DI_STR_treat", "DI_theta" ] }, { "page": "DI_compare", "title": "Compare a Fitted Diversity-Interactions Model to the Reference Model", "topics": [ "DI_compare" ] }, { "page": "DI_data_manipulation", "title": "Data manipulation function", "topics": [ "DI_data", "DI_data_ADD", "DI_data_E_AV", "DI_data_FG", "DI_data_fullpairwise", "DI_data_manipulation", "DI_data_prepare" ] }, { "page": "DI_methods", "title": "Methods for 'DI' Objects", "topics": [ "AIC.DI", "AICc.DI", "anova.DI", "BIC.DI", "BICc.DI", "fortify.DI", "logLik.DI" ] }, { "page": "DImodels-internal", "title": "Internal Functions", "topics": [ "add_name_check", "AIC2", "AICc", "AICc.default", "AICcsel_autoDI", "AICsel_autoDI", "anovaDIglm", "anova_glmlist", "autoDI_step0", "autoDI_step1", "autoDI_step2", "autoDI_step3", "autoDI_step4", "BIC2", "BICc", "BICc.default", "BICcsel_autoDI", "BICsel_autoDI", "DI_matrix_check", "DI_reference", "get_community", "get_P_indices", "get_theta_cols", "namesub_autoDI", "namesub_DI", "proflik_theta", "reftest_autoDI", "test_autoDI", "theta_index_matching" ] }, { "page": "extract", "title": "Extract terms from a DI or autoDI model object", "topics": [ "extract", "extract.autoDI", "extract.DI" ] }, { "page": "predict.DI", "title": "Predict Method for Diversity-Interactions (DI) Models", "topics": [ "predict.DI" ] }, { "page": "richness_vs_DI", "title": "Comparing the Richness Model with DI Alternatives", "topics": [ "richness_vs_DI" ] }, { "page": "sim0", "title": "The Simulated \"sim0\" Dataset", "topics": [ "sim0" ] }, { "page": "sim0_design", "title": "The \"sim0_design\" Dataset", "topics": [ "sim0_design" ] }, { "page": "sim1", "title": "The Simulated \"sim1\" Dataset", "topics": [ "sim1" ] }, { "page": "sim2", "title": "The Simulated \"sim2\" Dataset", "topics": [ "sim2" ] }, { "page": "sim3", "title": "The Simulated \"sim3\" Dataset", "topics": [ "sim3" ] }, { "page": "sim4", "title": "The Simulated \"sim4\" Dataset", "topics": [ "sim4" ] }, { "page": "sim5", "title": "The Simulated \"sim5\" Dataset", "topics": [ "sim5" ] }, { "page": "Switzerland", "title": "The \"Switzerland\" Dataset", "topics": [ "Switzerland" ] }, { "page": "theta_CI", "title": "Compute Confidence Interval for Theta", "topics": [ "theta_CI" ] }, { "page": "update_DI", "title": "Update DI function call", "topics": [ "update_DI" ] } ], "_readme": "https://github.com/rafamoral/dimodels/raw/HEAD/README.md", "_rundeps": [ "cli", "codetools", "cpp11", "farver", "ggplot2", "glue", "gtable", "hnp", "isoband", "labeling", "lattice", "lifecycle", "MASS", "Matrix", "multcomp", "multcompView", "mvtnorm", "R6", "RColorBrewer", "rlang", "rootSolve", "S7", "sandwich", "scales", "survival", "TH.data", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "DImodels.Rmd", "filename": "DImodels.html", "title": "DImodels", "engine": "knitr::rmarkdown", "headings": [ "Getting Started with DImodels", "DImodels installation and load", "Accessing an introduction to Diversity-Introductions models", "Datasets included in the DImodels package", "The sim3 dataset", "Exploring the data", "Implementing an automated DI model fitting process using autoDI", "Fitting individual models using the DI function", "Fitting the final model selected by autoDI using DI", "Re-fitting the final model selected by autoDI estimating theta using update_DI", "Grouping the species identity effects in the model", "Fitting customised models using the DI function", "Including treatment by species identity term interactions using extra_formula", "Including treatment by species interaction terms using extra_formula", "Fitting only a subset of the FG interaction terms using custom_formula", "Making predictions and testing contrasts for DI models", "Predictions using a DI model", "Uncertainity around predictions", "Contrasts for DI models", "Compact letter display (CLD) for community comparisons", "References" ], "created": "2023-03-07 18:26:26", "modified": "2025-08-05 08:05:04", "commits": 5 } ], "_score": 6.312177356439779, "_indexed": true, "_nocasepkg": "dimodels", "_universes": [ "rafamoral" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.3", "date": "2026-05-17T08:18:51.000Z", "distro": "noble", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "6eec11d1a486962c38640c6c46b435eb04000e1d5df85667c7d88f3054249698", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.6.0", "os": "linux", "version": "1.3.3", "date": "2026-05-17T08:18:41.000Z", "distro": "noble", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "934365abc0893f36ee32abd46b3d3dca334c8d290558510755bf5ae7900da0d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.5.3", "os": "mac", "version": "1.3.3", "date": "2026-05-17T08:18:44.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "fc43586d84368d202fa9412ed448c3552cb9e329d7a44f9d4e819fc4942788a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.6.0", "os": "mac", "version": "1.3.3", "date": "2026-05-17T08:18:33.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "df4c171c6d6a438a1fcf904f086bc57a003789212b1af2c5f3d1331901dfed4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.7.0", "os": "win", "version": "1.3.3", "date": "2026-05-17T08:17:53.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "ebe50a7c0900bdea359a96a6a71416154fcadb79da6fc6a67bbf804010fc5bf3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.5.3", "os": "win", "version": "1.3.3", "date": "2026-05-17T08:17:56.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "6c6ee8c4e50daa511e3e9989bce3514ceae6ca9ab902c164794fd77a9d68aafe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.6.0", "os": "win", "version": "1.3.3", "date": "2026-05-17T08:17:54.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "221037e97c33adb75fb0e81bcfccd3e02632e8c7664c1622affba2f483c08b67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.3", "date": "2026-06-02T17:18:24.000Z", "commit": "3d5ff8b4925d106e74f877b00932ae4ec4716f8b", "fileid": "7376fbb859606cb7bdfbfe3be97b892798c5a25ccb3aac748bb274f9f6378e0f", "status": "success", "buildurl": "https://github.com/r-universe/rafamoral/actions/runs/25985567838" } ] }