{ "_id": "6a229fefcd65a98ecbd58588", "Package": "mmodely", "Version": "0.2.5", "Date": "2023-05-05", "Title": "Modeling Multivariate Origins Determinants - Evolutionary\nLineages in Ecology", "Author": "David M Schruth", "Maintainer": "David M Schruth ", "Description": "Perform multivariate modeling of evolved traits, with\nspecial attention to understanding the interplay of the\nmulti-factorial determinants of their origins in complex\necological settings (Stephens, 2007\n). This software primarily\nconcentrates on phylogenetic regression analysis, enabling\nimplementation of tree transformation averaging and\nvisualization functionality. Functions additionally support\ninformation theoretic approaches (Grueber, 2011\n; Garamszegi, 2011\n) such as model averaging and\nselection of phylogenetic models. Accessory functions are also\nimplemented for coef standardization (Cade 2015), selection\nuncertainty, and variable importance (Burnham & Anderson 2000).\nThere are other numerous functions for visualizing confounded\nvariables, plotting phylogenetic trees, as well as reporting\nand exporting modeling results. Lastly, as challenges to\necology are inherently multifarious, and therefore often\nmulti-dataset, this package features several functions to\nsupport the identification, interpolation, merging, and\nupdating of missing data and outdated nomenclature.", "License": "Apache License", "LazyLoad": "yes", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 10:04:22 UTC", "User": "root" }, "Repository": "https://dranthropoid.r-universe.dev", "Date/Publication": "2023-05-17 06:10:02 UTC", "RemoteUrl": "https://github.com/cran/mmodely", "RemoteRef": "HEAD", "RemoteSha": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "MD5sum": "6f1a279407890598e584868fcccaae69", "_user": "dranthropoid", "_type": "src", "_file": "mmodely_0.2.5.tar.gz", "_fileid": "65947280281bc9fb619180abf89f2dc8216d61ea23d9f6d5ea41375001d90b27", "_filesize": 546300, "_sha256": "65947280281bc9fb619180abf89f2dc8216d61ea23d9f6d5ea41375001d90b27", "_created": "2026-06-05T10:04:22.000Z", "_published": "2026-06-05T10:07:43.007Z", "_distro": "noble", "_jobs": [ { "job": 79706458680, "time": 110, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7434020032" }, { "job": 79706459024, "time": 113, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7434021106" }, { "job": 79706458766, "time": 165, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7434028803" }, { "job": 79706458665, "time": 127, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7434018889" }, { "job": 79705990728, "time": 180, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7433987195" }, { "job": 79706458677, "time": 93, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7434015157" }, { "job": 79706458709, "time": 78, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7434010943" }, { "job": 79706458657, "time": 73, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7434009187" }, { "job": 79706458751, "time": 77, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7434010424" } ], "_buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/mmodely", "_commit": { "id": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "author": "David M Schruth ", "committer": "cran-robot ", "message": "version 0.2.5\n", "time": 1684303802 }, "_maintainer": { "name": "David M Schruth", "email": "dschruth@anthropoidea.org", "login": "dranthropoid", "twitter": "@dranthropoid", "description": "Computational Ecologist using primate data to investigate anthropoid evolution and anthropology (of humans)", "uuid": 67233 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.0.0", "role": "Depends" }, { "package": "caper", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "caroline", "role": "Imports" }, { "package": "ape", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "dranthropoid", "count": 3, "uuid": 67233 } ], "_userbio": { "uuid": 67233, "type": "user", "name": "David Schruth", "description": "Computational Ecologist using primate data to investigate anthropoid evolution and anthropology (of humans)" }, "_downloads": { "count": 175, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mmodely" }, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mmodely.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "dranthropoid", "_cranurl": false, "_releases": [ { "version": "0.2.0", "date": "2022-11-04" }, { "version": "0.2.2", "date": "2022-11-06" }, { "version": "0.2.5", "date": "2023-05-17" } ], "_exports": [ "average.fit.models", "calc.q2n.ratio", "cept", "comp.data", "compare.data.gs.vs.tree.tips", "correct.AIC", "count.mod.vars", "ct.possible.models", "drop.na.data", "fit.1ln.rprt", "get.mod.clmns", "get.mod.outcome", "get.mod.vars", "get.model.combos", "get.pgls.coefs", "get.phylo.stats", "gs.check", "gs.names.mismatch.check", "gs.rename", "interpolate", "missing.data", "missing.fill.in", "pgls.iter", "pgls.iter.stats", "pgls.print", "pgls.report", "pgls.wrap", "plot.confound.grid", "plot.pgls.iters", "plot.pgls.R2AIC", "plot.transformed.phylo", "plot.xy.ab.p", "select.best.models", "sparge.modsel", "trim.phylo", "variable.importance", "weight.IC" ], "_help": [ { "page": "average.fit.models", "title": "Calculate a weighted average of pglm", "topics": [ "average.fit.models", "variable.importance" ] }, { "page": "calc.q2n.ratio", "title": "Calculate the ratio of fit predictor variables to sample size", "topics": [ "calc.q2n.ratio" ] }, { "page": "cept", "title": "Include all variables except ...", "topics": [ "cept" ] }, { "page": "comp.data", "title": "Comparative Data", "topics": [ "comp.data" ] }, { "page": "compare.data.gs.vs.tree.tips", "title": "Find data being dropped by mismatches to the tree", "topics": [ "compare.data.gs.vs.tree.tips" ] }, { "page": "correct.AIC", "title": "Correct AIC", "topics": [ "correct.AIC" ] }, { "page": "count.mod.vars", "title": "Count the predictor variables in a model", "topics": [ "count.mod.vars" ] }, { "page": "ct.possible.models", "title": "Count all possible model combinations", "topics": [ "ct.possible.models" ] }, { "page": "drop.na.data", "title": "Drop any rows with NA values", "topics": [ "drop.na.data" ] }, { "page": "fit.1ln.rprt", "title": "Report a model fit in a single line of text output", "topics": [ "fit.1ln.rprt" ] }, { "page": "get.mod.clmns", "title": "Get model columns", "topics": [ "get.mod.clmns" ] }, { "page": "get.mod.outcome", "title": "Get the outcome variable from a model string", "topics": [ "get.mod.outcome" ] }, { "page": "get.mod.vars", "title": "Get model variable names", "topics": [ "get.mod.vars" ] }, { "page": "get.model.combos", "title": "All combinations of predictor variables", "topics": [ "get.model.combos" ] }, { "page": "get.pgls.coefs", "title": "Get coeficients from a list of PGLS model-fits (from each selected subset)", "topics": [ "get.pgls.coefs" ] }, { "page": "get.phylo.stats", "title": "Get tree statistics for a trait", "topics": [ "get.phylo.stats" ] }, { "page": "gs.check", "title": "Check \"Genus species\" name formatting", "topics": [ "gs.check" ] }, { "page": "gs.names.mismatch.check", "title": "Check \"Genus species\" name formatting", "topics": [ "gs.names.mismatch.check" ] }, { "page": "gs.rename", "title": "Rename the Genus species information in a data frame", "topics": [ "gs.rename" ] }, { "page": "interpolate", "title": "Interpolate missing data in a data frame", "topics": [ "interpolate" ] }, { "page": "missing.data", "title": "Report missing values in a dataframe", "topics": [ "missing.data" ] }, { "page": "missing.fill.in", "title": "Fill in missing values in a dataframe with a secondary source", "topics": [ "missing.fill.in" ] }, { "page": "pgls.iter", "title": "Iterate through PGLS estimations", "topics": [ "pgls.iter" ] }, { "page": "pgls.iter.stats", "title": "Statistics from PGLS runs", "topics": [ "pgls.iter.stats" ] }, { "page": "pgls.print", "title": "Print the results of a PGLS model fit", "topics": [ "pgls.print" ] }, { "page": "pgls.report", "title": "Report PGLS results as a table", "topics": [ "pgls.report" ] }, { "page": "pgls.wrap", "title": "A Wrapper for PGLS model", "topics": [ "pgls.wrap" ] }, { "page": "plot.confound.grid", "title": "Plot a grid of x y plots split by a confounder z", "topics": [ "plot.confound.grid" ] }, { "page": "plot.pgls.iters", "title": "Plot the PGLS iterations", "topics": [ "plot.pgls.iters" ] }, { "page": "plot.pgls.R2AIC", "title": "Plot (R2 vs AIC) results of a collection of fit PGLS models", "topics": [ "plot.pgls.R2AIC" ] }, { "page": "plot.transformed.phylo", "title": "Plot a transformed phylogenetic tree", "topics": [ "plot.transformed.phylo" ] }, { "page": "plot.xy.ab.p", "title": "An x/y scatterplot with a linear regression line and p-value", "topics": [ "plot.xy.ab.p" ] }, { "page": "select.best.models", "title": "Get the best model from list of PGLS model fits", "topics": [ "select.best.models" ] }, { "page": "sparge.modsel", "title": "Coeficients distribution [sparge] plot of models selected from each subset", "topics": [ "sparge.modsel" ] }, { "page": "trim.phylo", "title": "Trim a phylogenetic tree using Genus species names", "topics": [ "trim.phylo" ] }, { "page": "weight.IC", "title": "Get IC weights", "topics": [ "weight.IC" ] } ], "_rundeps": [ "ape", "caper", "caroline", "digest", "lattice", "MASS", "mvtnorm", "nlme", "Rcpp" ], "_vignettes": [ { "source": "Schruth-mmodely-vignette-Vision.Rnw", "filename": "Schruth-mmodely-vignette-Vision.pdf", "title": "Information-theoretic PGLS model selection workflow: a primate vision example", "engine": "utils::Sweave", "headings": [], "created": "2022-11-04 09:00:06", "modified": "2023-05-17 06:10:02", "commits": 3 }, { "source": "Schruth-mmodely-vignette-Vocal.Rnw", "filename": "Schruth-mmodely-vignette-Vocal.pdf", "title": "Information-theoretic PGLS model selection workflow: a primate vocal communication example", "engine": "utils::Sweave", "headings": [], "created": "2022-11-04 09:00:06", "modified": "2023-05-17 06:10:02", "commits": 3 } ], "_score": 2.3010299956639813, "_indexed": true, "_nocasepkg": "mmodely", "_universes": [ "dranthropoid" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.5", "date": "2026-06-05T10:06:07.000Z", "distro": "noble", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "17baa304a0b7f1b5c9495a87fd9406090015e4adaad7d30459f3803d89130ccb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.6.0", "os": "linux", "version": "0.2.5", "date": "2026-06-05T10:06:10.000Z", "distro": "noble", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "5febd6c4aa4a33b6fabe9442a70d9ccf7c7bc02ad349950500bc67a5032d168b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.5.3", "os": "mac", "version": "0.2.5", "date": "2026-06-05T10:06:45.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "f97f18d1af9cd8d422c2024c1f4141e35e91c099cddaf443b849cee6bea226e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.6.0", "os": "mac", "version": "0.2.5", "date": "2026-06-05T10:06:10.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "93ebe2d8222af6338e97940ad74ae21986dddfa836413fbd140847879963b178", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.5", "date": "2026-06-05T10:06:11.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "b34bf861c7dcdeae9ad5c5a40cc80f1b717908dd9c20ccb5c82b9a7a9b546351", "status": "success", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.7.0", "os": "win", "version": "0.2.5", "date": "2026-06-05T10:05:27.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "8ef34dd9f39414c7e3006c1824d58736f0fd845ea01d36eb95d8cd1f17e0a25a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.5.3", "os": "win", "version": "0.2.5", "date": "2026-06-05T10:05:25.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "0236e8f8d6dee552d6e7dc8d3f49a4cb16b73fe57cb66d4db299a5f79c362625", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" }, { "r": "4.6.0", "os": "win", "version": "0.2.5", "date": "2026-06-05T10:05:27.000Z", "commit": "b434e85c5b6b0f2dedac7aa0cb87dfc4842755b6", "fileid": "01ce54f2f826037d32d8000cfd7f685a556c6b3a720e96374bb7869cf38e1674", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/dranthropoid/actions/runs/27008472684" } ] }