{ "_id": "6a11559aacfb0bcc41ceb151", "Package": "zetadiv", "Title": "Functions to Compute Compositional Turnover Using Zeta Diversity", "Version": "1.3.0", "Date": "2025-05-27", "Authors@R": "c(\nperson(\"Guillaume\", \"Latombe\", email = \"latombe.guillaume@gmail.com\", role=c(\"aut\",\"cre\")),\nperson(\"Melodie A.\", \"McGeoch\", role=c(\"aut\")),\nperson(\"David A.\", \"Nipperess\", role=c(\"aut\")),\nperson(\"Cang\", \"Hui\", role=c(\"aut\")))", "Description": "Functions to compute compositional turnover using\nzeta-diversity, the number of species shared by multiple\nassemblages. The package includes functions to compute\nzeta-diversity for a specific number of assemblages and to\ncompute zeta-diversity for a range of numbers of assemblages.\nIt also includes functions to explain how zeta-diversity varies\nwith distance and with differences in environmental variables\nbetween assemblages, using generalised linear models, linear\nmodels with negative constraints, generalised additive\nmodels,shape constrained additive models, and I-splines.", "License": "GPL-3", "LazyData": "true", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 07:18:07 UTC", "User": "root" }, "Author": "Guillaume Latombe [aut, cre], Melodie A. McGeoch [aut], David\nA. Nipperess [aut], Cang Hui [aut]", "Maintainer": "Guillaume Latombe ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-05-28 10:30:02 UTC", "RemoteUrl": "https://github.com/cran/zetadiv", "RemoteRef": "HEAD", "RemoteSha": "3a3e592d77a810e0d074d1483d2a68db9017739a", "MD5sum": "c5284d03cbebc1512d0020a1cef34351", "_user": "cran", "_type": "src", "_file": "zetadiv_1.3.0.tar.gz", "_fileid": "4bd7c00834436a6af70d4c655f613e911d4d7560f522aff9912fc68fa8a90cfa", "_filesize": 409103, "_sha256": "4bd7c00834436a6af70d4c655f613e911d4d7560f522aff9912fc68fa8a90cfa", "_created": "2026-05-23T07:18:07.000Z", "_published": "2026-05-23T07:22:02.380Z", "_distro": "noble", "_jobs": [ { "job": 77505799705, "time": 192, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175262998" }, { "job": 77505799695, "time": 189, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175262677" }, { "job": 77505629484, "time": 189, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175244901" }, { "job": 77505799681, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175256400" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26326679923", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/zetadiv", "_commit": { "id": "3a3e592d77a810e0d074d1483d2a68db9017739a", "author": "Guillaume Latombe ", "committer": "cran-robot ", "message": "version 1.3.0\n", "time": 1748428202 }, "_maintainer": { "name": "Guillaume Latombe", "email": "latombe.guillaume@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "scam", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "geodist", "role": "Imports" }, { "package": "nnls", "role": "Imports" }, { "package": "glm2", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-22", "n": 1 } ], "_tags": [ { "name": "1.3.0", "date": "2025-05-28" } ], "_stars": 3, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 557, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/zetadiv" }, "_mentions": 4, "_searchresults": 81, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/zetadiv.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1", "date": "2015-06-04" }, { "version": "1.0", "date": "2016-12-09" }, { "version": "1.0.1", "date": "2017-06-06" }, { "version": "1.1.0", "date": "2018-04-11" }, { "version": "1.1.1", "date": "2018-05-17" }, { "version": "1.2.0", "date": "2020-07-02" }, { "version": "1.2.1", "date": "2022-06-10" }, { "version": "1.3.0", "date": "2025-05-28" } ], "_exports": [ "glm.cons", "glm.fit.cons", "Ispline", "pie.neg", "Plot.ispline", "Plot.zeta.ddecay", "Plot.zeta.ddecays", "Plot.zeta.decline", "Plot.zeta.scale.min.dist", "Plot.zeta.scale.regular", "Predict.msgdm", "Reg.ispline", "rescale.min.dist", "rescale.regular", "Return.ispline", "Zeta.ddecay", "Zeta.ddecays", "Zeta.decline.ex", "Zeta.decline.mc", "Zeta.msgdm", "Zeta.order.ex", "Zeta.order.mc", "Zeta.order.mc.mult", "Zeta.sam.sensitivity", "Zeta.scale.min.dist", "Zeta.scale.regular", "Zeta.varpart" ], "_datasets": [ { "name": "bird.env.coarse", "title": "South-East Australia Environmental Dataset at Coarse Scale", "object": "bird.env.coarse", "class": [ "data.frame" ], "fields": [ "x", "y", "Natural", "Irrigated", "Water", "Elevation", "ApP", "Temp", "Precip" ], "rows": 123, "table": true, "tojson": true }, { "name": "bird.env.fine", "title": "South-East Australia Environmental Dataset at Fine Scale", "object": "bird.env.fine", "class": [ "data.frame" ], "fields": [ "x", "y", "Natural", "Irrigated", "Water", "Elevation", "ApP", "Temp", "Precip" ], "rows": 604, "table": true, "tojson": true }, { "name": "bird.spec.coarse", "title": "Australia Bird Atlas Species Occurrence Dataset at Coarse Scale over South-East Australia", "object": "bird.spec.coarse", "class": [ "data.frame" ], "fields": [ "x", "y", "Apostlebird", "Australasian Figbird", "Australasian Pipit", "Australian Bustard", "Australian Hobby", "Australian Logrunner", "Australian Magpie", "Australian Raven", "Australian Ringneck", "Australian Swiftlet", "Azure Kingfisher", "Banded Whiteface", "Barbary Dove", "Bassian Thrush", "Beautiful Firetail", "Bell Miner", "Black Falcon", "Black Honeyeater", "Black Kite", "Blue Bonnet", "Brahminy Kite", "Brown Falcon", "Brown Gerygone", "Brown Goshawk", "Brown Honeyeater", "Brown Quail", "Brown Songlark", "Brown Thornbill", "Brown Treecreeper", "Brush Bronzewing", "Brush Cuckoo", "Budgerigar", "Chiming Wedgebill", "Chirruping Wedgebill", "Cicadabird", "Cockatiel", "Collared Kingfisher", "Collared Sparrowhawk", "Common Bronzewing", "Corella species", "Crescent Honeyeater", "Crested Bellbird", "Crested Pigeon", "Crimson Chat", "Crimson Rosella", "Crow & Raven species", "Diamond Dove", "Diamond Firetail", "Dollarbird", "Dusky Honeyeater", "Dusky Robin", "Dusky Woodswallow", "Eastern Bristlebird", "Eastern Koel", "Eastern Osprey", "Eastern Rosella", "Eastern Spinebill", "Eastern Whipbird", "Eastern Yellow Robin", "Elegant Parrot", "Emerald Dove", "Emu", "Eyrean Grasswren", "Fairy Gerygone", "Fairy Martin", "Flame Robin", "Flock Bronzewing", "Forest Kingfisher", "Forest Raven", "Fuscous Honeyeater", "Galah", "Gibberbird", "Golden Whistler", "Green Catbird", "Green Rosella", "Grey Butcherbird", "Grey Currawong", "Grey Falcon", "Grey Fantail", "Grey Goshawk", "Grey Grasswren", "Ground Parrot", "Hooded Robin", "Inland Thornbill", "Jacky Winter", "King Quail", "Laughing Kookaburra", "Leaden Flycatcher", "Little Corella", "Little Crow", "Little Eagle", "Little Friarbird", "Little Grassbird", "Little Lorikeet", "Little Raven", "Little Wattlebird", "Little Woodswallow", "Malleefowl", "Mangrove Gerygone", "Mangrove Honeyeater", "Masked Woodswallow", "Mistletoebird", "Mulga Parrot", "Musk Lorikeet", "Nankeen Kestrel", "New Holland Honeyeater", "Noisy Friarbird", "Noisy Miner", "Noisy Pitta", "Northern Pintail", "Olive Whistler", "Orange Chat", "Oriental Cuckoo", "Pacific Baza", "Painted Finch", "Painted Honeyeater", "Pallid Cuckoo", "Paradise Riflebird", "Peaceful Dove", "Peregrine Falcon", "Pheasant Coucal", "Pied Butcherbird", "Pied Currawong", "Pied Honeyeater", "Pilotbird", "Pink Robin", "Rainbow Lorikeet", "Red Goshawk", "Red Wattlebird", "Redthroat", "Regent Bowerbird", "Regent Honeyeater", "Regent Parrot", "Restless Flycatcher", "Rock Parrot", "Rockwarbler", "Rose Robin", "Rufous Bristlebird", "Rufous Fantail", "Rufous Fieldwren", "Rufous Songlark", "Rufous Treecreeper", "Rufous Whistler", "Russet-tailed Thrush", "Sacred Kingfisher", "Satin Bowerbird", "Satin Flycatcher", "Scarlet Honeyeater", "Scarlet Robin", "Short-tailed Grasswren", "Shy Heathwren", "Silvereye", "Singing Honeyeater", "Southern Whiteface", "Spangled Drongo", "Speckled Warbler", "Spectacled Monarch", "Spotted Bowerbird", "Spotted Harrier", "Spotted Pardalote", "Squatter Pigeon", "Striated Fieldwren", "Striated Grasswren", "Striated Pardalote", "Striated Thornbill", "Striped Honeyeater", "Stubble Quail", "Superb Lyrebird", "Superb Parrot", "Swamp Harrier", "Swift Parrot", "Tawny Grassbird", "Topknot Pigeon", "Torresian Crow", "Tree Martin", "Turquoise Parrot", "Varied Honeyeater", "Varied Sittella", "Varied Triller", "Weebill", "Welcome Swallow", "Western Gerygone", "Western Whipbird", "Western Yellow Robin", "Whistling Kite", "Willie Wagtail", "Wonga Pigeon", "Yellow Chat", "Yellow Thornbill", "Yellow Wattlebird", "Zebra Finch" ], "rows": 123, "table": true, "tojson": true }, { "name": "bird.spec.fine", "title": "Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australia", "object": "bird.spec.fine", "class": [ "data.frame" ], "fields": [ "x", "y", "Apostlebird", "Australasian Figbird", "Australasian Pipit", "Australian Bustard", "Australian Hobby", "Australian Logrunner", "Australian Magpie", "Australian Raven", "Australian Ringneck", "Australian Swiftlet", "Azure Kingfisher", "Banded Whiteface", "Barbary Dove", "Bassian Thrush", "Beautiful Firetail", "Bell Miner", "Black Falcon", "Black Honeyeater", "Black Kite", "Blue Bonnet", "Brahminy Kite", "Brown Falcon", "Brown Gerygone", "Brown Goshawk", "Brown Honeyeater", "Brown Quail", "Brown Songlark", "Brown Thornbill", "Brown Treecreeper", "Brush Bronzewing", "Brush Cuckoo", "Budgerigar", "Chirruping Wedgebill", "Cicadabird", "Cockatiel", "Collared Kingfisher", "Collared Sparrowhawk", "Common Bronzewing", "Corella species", "Crescent Honeyeater", "Crested Bellbird", "Crested Pigeon", "Crimson Chat", "Crimson Rosella", "Crow & Raven species", "Diamond Dove", "Diamond Firetail", "Dollarbird", "Dusky Honeyeater", "Dusky Woodswallow", "Eastern Bristlebird", "Eastern Koel", "Eastern Osprey", "Eastern Rosella", "Eastern Spinebill", "Eastern Whipbird", "Eastern Yellow Robin", "Elegant Parrot", "Emerald Dove", "Emu", "Eyrean Grasswren", "Fairy Gerygone", "Fairy Martin", "Flame Robin", "Flock Bronzewing", "Forest Kingfisher", "Forest Raven", "Fuscous Honeyeater", "Galah", "Gibberbird", "Golden Whistler", "Green Catbird", "Green Rosella", "Grey Butcherbird", "Grey Currawong", "Grey Falcon", "Grey Fantail", "Grey Goshawk", "Grey Grasswren", "Ground Parrot", "Hooded Robin", "Inland Thornbill", "Jacky Winter", "King Quail", "Laughing Kookaburra", "Leaden Flycatcher", "Little Corella", "Little Crow", "Little Eagle", "Little Friarbird", "Little Grassbird", "Little Lorikeet", "Little Raven", "Little Wattlebird", "Little Woodswallow", "Malleefowl", "Mangrove Gerygone", "Mangrove Honeyeater", "Masked Woodswallow", "Mistletoebird", "Mulga Parrot", "Musk Lorikeet", "Nankeen Kestrel", "New Holland Honeyeater", "Noisy Friarbird", "Noisy Miner", "Noisy Pitta", "Northern Pintail", "Olive Whistler", "Orange Chat", "Oriental Cuckoo", "Pacific Baza", "Painted Finch", "Painted Honeyeater", "Pallid Cuckoo", "Paradise Riflebird", "Peaceful Dove", "Peregrine Falcon", "Pheasant Coucal", "Pied Butcherbird", "Pied Currawong", "Pied Honeyeater", "Pilotbird", "Pink Robin", "Princess Parrot", "Rainbow Lorikeet", "Red Wattlebird", "Redthroat", "Regent Bowerbird", "Regent Honeyeater", "Regent Parrot", "Restless Flycatcher", "Rock Parrot", "Rockwarbler", "Rose Robin", "Rufous Bristlebird", "Rufous Fantail", "Rufous Fieldwren", "Rufous Songlark", "Rufous Treecreeper", "Rufous Whistler", "Russet-tailed Thrush", "Sacred Kingfisher", "Satin Bowerbird", "Satin Flycatcher", "Scarlet Honeyeater", "Scarlet Robin", "Shining Flycatcher", "Short-tailed Grasswren", "Shy Heathwren", "Silvereye", "Singing Honeyeater", "Southern Whiteface", "Spangled Drongo", "Speckled Warbler", "Spectacled Monarch", "Spotted Bowerbird", "Spotted Harrier", "Spotted Pardalote", "Squatter Pigeon", "Striated Fieldwren", "Striated Grasswren", "Striated Pardalote", "Striated Thornbill", "Striped Honeyeater", "Stubble Quail", "Superb Lyrebird", "Superb Parrot", "Swamp Harrier", "Swift Parrot", "Tawny Grassbird", "Topknot Pigeon", "Torresian Crow", "Tree Martin", "Turquoise Parrot", "Varied Honeyeater", "Varied Sittella", "Varied Triller", "Weebill", "Welcome Swallow", "Western Gerygone", "Western Whipbird", "Western Yellow Robin", "Whistling Kite", "Willie Wagtail", "Wonga Pigeon", "Yellow Chat", "Yellow Oriole", "Yellow Thornbill", "Zebra Finch" ], "rows": 604, "table": true, "tojson": true }, { "name": "Marion.env", "title": "Marion Island Environmental Dataset", "object": "Marion.env", "class": [ "data.frame" ], "fields": [ "x", "y", "Altitude", "Side" ], "rows": 12, "table": true, "tojson": true }, { "name": "Marion.species", "title": "Marion Island Species Presence-Absence Dataset", "object": "Marion.species", "class": [ "data.frame" ], "fields": [ "x", "y", "Eupodes.minutus", "Acari.sp1", "Acari.sp3", "Acari.sp4", "Rhodacaridae", "Dendrolaelaps.sp", "Cilibidae.sp", "Nanorchestes.sp", "Rhagidia.sp", "Ereynetes.macquariensis", "Tydeidae", "Bdellodes.sp", "Eryngiopus.sp.", "Oribatid.a", "Liochthonius.australis", "Maquarioppia.striata", "Austroppia.crozetensis", "Halozetes.fulvus", "Dometorina.marionensis", "Swiebea.talpa", "Algophagus.sp1", "Algophagus.sp2", "Tullbergia.bisetosa", "Isotoma.marionensis", "Cryptopygus.dubius", "C..antarcticus", "C..ceacus", "Isotomurus.palustris", "Megalothorax.sp", "Sminthurinus.tuberculatus", "S..granulosus" ], "rows": 12, "table": true, "tojson": true } ], "_help": [ { "page": "bird.env.coarse", "title": "South-East Australia Environmental Dataset at Coarse Scale", "topics": [ "bird.env.coarse" ] }, { "page": "bird.env.fine", "title": "South-East Australia Environmental Dataset at Fine Scale", "topics": [ "bird.env.fine" ] }, { "page": "bird.spec.coarse", "title": "Australia Bird Atlas Species Occurrence Dataset at Coarse Scale over South-East Australia", "topics": [ "bird.spec.coarse" ] }, { "page": "bird.spec.fine", "title": "Australia Bird Atlas Species Occurrence Dataset at Fine Scale over South-East Australia", "topics": [ "bird.spec.fine" ] }, { "page": "glm.cons", "title": "Fitting Generalized Linear Models with constraint on the coefficients signs", "topics": [ "glm.cons" ] }, { "page": "glm.fit.cons", "title": "Generalized Linear Models fitting method with negative coefficients constraint", "topics": [ "glm.fit.cons" ] }, { "page": "Ispline", "title": "Transform data using I-splines", "topics": [ "Ispline" ] }, { "page": "Marion.env", "title": "Marion Island Environmental Dataset", "topics": [ "Marion.env" ] }, { "page": "Marion.species", "title": "Marion Island Species Presence-Absence Dataset", "topics": [ "Marion.species" ] }, { "page": "pie.neg", "title": "Pie Chart, considering negative values as zeros", "topics": [ "pie.neg" ] }, { "page": "Plot.ispline", "title": "Plots I-splines for Multi-Site Generalised Dissimilarity Modelling", "topics": [ "Plot.ispline" ] }, { "page": "Plot.zeta.ddecay", "title": "Zeta distance-decay plotting", "topics": [ "Plot.zeta.ddecay" ] }, { "page": "Plot.zeta.ddecays", "title": "Zeta distance-decay plotting for multiple orders", "topics": [ "Plot.zeta.ddecays" ] }, { "page": "Plot.zeta.decline", "title": "Zeta diversity decline plotting", "topics": [ "Plot.zeta.decline" ] }, { "page": "Plot.zeta.scale.min.dist", "title": "Plotting of zeta diversity scaling with sample grain dependency based on the minimum distance between sites", "topics": [ "Plot.zeta.scale.min.dist" ] }, { "page": "Plot.zeta.scale.regular", "title": "Plotting of zeta diversity scaling with sample grain using hierarchical increases in grain size", "topics": [ "Plot.zeta.scale.regular" ] }, { "page": "Predict.msgdm", "title": "Predict zeta values for new environmental and distance data", "topics": [ "Predict.msgdm" ] }, { "page": "Reg.ispline", "title": "Perform an I-spline regression", "topics": [ "Reg.ispline" ] }, { "page": "rescale.min.dist", "title": "Rescaling of data based on the minimum distance between sites", "topics": [ "rescale.min.dist" ] }, { "page": "rescale.regular", "title": "Rescaling of data following a hierarchical increase in grain size", "topics": [ "rescale.regular" ] }, { "page": "Return.ispline", "title": "Computing splines coordinates from I-spline-based multi-site generalised dissimilarity modelling", "topics": [ "Return.ispline" ] }, { "page": "Zeta.ddecay", "title": "Zeta distance decay for a specific number of assemblages or sites", "topics": [ "Zeta.ddecay" ] }, { "page": "Zeta.ddecays", "title": "Zeta distance decay for a range of numbers of assemblages or sites", "topics": [ "Zeta.ddecays" ] }, { "page": "Zeta.decline.ex", "title": "Expectation of zeta diversity decline", "topics": [ "Zeta.decline.ex" ] }, { "page": "Zeta.decline.mc", "title": "Zeta diversity decline using Monte Carlo sampling", "topics": [ "Zeta.decline.mc" ] }, { "page": "Zeta.msgdm", "title": "Multi-site generalised dissimilarity modelling for a set of environmental variables and distances", "topics": [ "Zeta.msgdm" ] }, { "page": "Zeta.order.ex", "title": "Expectation of zeta diversity for a specific number of assemblages or sites", "topics": [ "Zeta.order.ex" ] }, { "page": "Zeta.order.mc", "title": "Zeta diversity for a specific number of assemblages or sites using Monte Carlo sampling", "topics": [ "Zeta.order.mc" ] }, { "page": "Zeta.order.mc.mult", "title": "Number of species in common between a specific number of assemblages or sites using Monte Carlo sampling, for multiple combinations and several groups of taxa", "topics": [ "Zeta.order.mc.mult" ] }, { "page": "Zeta.sam.sensitivity", "title": "Sensitivity analysis for the sample size of zeta", "topics": [ "Zeta.sam.sensitivity" ] }, { "page": "Zeta.scale.min.dist", "title": "Zeta diversity scaling with sample grain dependency based on the minimum distance between sites", "topics": [ "Zeta.scale.min.dist" ] }, { "page": "Zeta.scale.regular", "title": "Zeta diversity scaling with sample grain using hierarchical increases in grain size", "topics": [ "Zeta.scale.regular" ] }, { "page": "Zeta.varpart", "title": "Variation partitioning for zeta diversity", "topics": [ "Zeta.varpart" ] } ], "_rundeps": [ "abind", "backports", "boot", "broom", "car", "carData", "cli", "cluster", "colorspace", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "generics", "geodist", "ggplot2", "glm2", "glue", "gtable", "isoband", 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