{ "_id": "6a587d3fff0138dec5d74281", "Package": "phylosem", "Type": "Package", "Title": "Phylogenetic Structural Equation Model", "Version": "1.1.4", "Date": "2024-04-02", "Authors@R": "c(person(given = \"James\",\nfamily = \"Thorson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"James.Thorson@noaa.gov\",\ncomment = c(ORCID = \"0000-0001-7415-1010\")),\nperson(given = \"Wouter\",\nfamily = \"van der Bijl\",\nrole = c(\"ctb\"),\nemail = \"wouter@zoology.ubc.ca\",\ncomment = c(ORCID = \"0000-0002-7366-1868\"))\n)", "Description": "Applies phylogenetic comparative methods (PCM) and\nphylogenetic trait imputation using structural equation models\n(SEM), extending methods from Thorson et al. (2023)\n. This implementation includes a\nminimal set of features, to allow users to easily read all of\nthe documentation and source code. PCM using SEM includes\nphylogenetic linear models and structural equation models as\nnested submodels, but also allows imputation of missing values.\nFeatures and comparison with other packages are described in\nThorson and van der Bijl (2023) .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://james-thorson-noaa.github.io/phylosem/", "BugReports": "https://github.com/James-Thorson-NOAA/phylosem/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libxml2-dev libssl-dev", "Repository": "https://noaa-fisheries-integrated-toolbox.r-universe.dev", "Date/Publication": "2025-03-11 17:26:02 UTC", "RemoteUrl": "https://github.com/James-Thorson-NOAA/phylosem", "RemoteRef": "HEAD", "RemoteSha": "321fc949e6fcde4a93c112d004afda997c636504", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-16 06:29:20 UTC", "User": "root" }, "Author": "James Thorson [aut, cre] (ORCID:\n),\nWouter van der Bijl [ctb] (ORCID:\n)", "Maintainer": "James Thorson ", "_user": "noaa-fisheries-integrated-toolbox", "_type": "src", "_file": "phylosem_1.1.4.tar.gz", "_fileid": "https://r2.ropensci.org/61bb9eb1ea6e63808e9bc3a6b6890e80f5d47d95b41aca1656ae8244018473c9", "_filesize": 1460360, "_sha256": "61bb9eb1ea6e63808e9bc3a6b6890e80f5d47d95b41aca1656ae8244018473c9", "_expires": "2026-10-24T06:42:05.000Z", "_created": "2026-07-16T06:29:20.000Z", "_published": "2026-07-16T06:42:07.675Z", "_jobs": [ { "job": 87551851561, "time": 307, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8367000827" }, { "job": 87551851613, "time": 401, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8367028982" }, { "job": 87551851599, "time": 347, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8367013292" }, { "job": 87551851672, "time": 346, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8367011771" }, { "job": 87551851612, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8366957473" }, { "job": 87551851635, "time": 639, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8367103208" }, { "job": 87551851588, "time": 189, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8366964746" }, { "job": 87551851618, "time": 376, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8367021188" }, { "job": 87549923574, "time": 774, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8366905624" }, { "job": 87551851602, "time": 230, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 87551851537, "time": 326, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8367006710" }, { "job": 87551851517, "time": 304, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8366998789" }, { "job": 87551851587, "time": 321, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8367004659" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564", "_status": "success", "_upstream": "https://github.com/James-Thorson-NOAA/phylosem", "_commit": { "id": "321fc949e6fcde4a93c112d004afda997c636504", "author": "Jim Thorson <50178738+James-Thorson-NOAA@users.noreply.github.com>", "committer": "GitHub ", "message": "Update README.md", "time": 1741713962 }, "_maintainer": { "name": "James Thorson", "email": "james.thorson@noaa.gov", "login": "james-thorson-noaa", "orcid": "0000-0001-7415-1010", "description": "", "uuid": 50178738 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "TMB", "role": "Depends" }, { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "TMB", "role": "LinkingTo" }, { "package": "sem", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "phylobase", "role": "Imports" }, { "package": "phylopath", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "semPlot", "role": "Suggests" }, { "package": "TreeTools", "role": "Suggests" }, { "package": "Rphylopars", "role": "Suggests" }, { "package": "phylolm", "role": "Suggests" }, { "package": "fishtree", "role": "Suggests" }, { "package": "phyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "phylosignal", "role": "Suggests" }, { "package": "adephylo", "role": "Suggests" }, { "package": "phytools", "role": "Enhances" }, { "package": "DiagrammeR", "role": "Enhances" } ], "_owner": "james-thorson-noaa", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "james-thorson-noaa", "count": 101, "uuid": 50178738 }, { "user": "ax3man", "count": 4, "uuid": 15309336 } ], "_userbio": { "uuid": 49974461, "type": "organization", "name": "NOAA Fisheries Integrated Toolbox", "followers": 9, "description": "GitHub Organization to manage the NOAA FIT" }, "_downloads": { "count": 296, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phylosem" }, "_devurl": "https://github.com/james-thorson-noaa/phylosem", "_pkgdown": "https://james-thorson-noaa.github.io/phylosem/", "_searchresults": 22, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/phylosem.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/james-thorson-noaa/phylosem", "_realowner": "james-thorson-noaa", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-08-25" }, { "version": "1.0.1", "date": "2023-09-19" }, { "version": "1.0.2", "date": "2023-09-23" }, { "version": "1.1.0", "date": "2023-10-06" }, { "version": "1.1.1", "date": "2023-11-26" }, { "version": "1.1.2", "date": "2023-12-20" }, { "version": "1.1.3", "date": "2024-02-01" }, { "version": "1.1.4", "date": "2024-04-02" } ], "_exports": [ "as_fitted_DAG", "as_phylo4d", "as_sem", "average", "best", "choice", "compare_phylosem", "list_parameters", "phylosem", "phylosem_control" ], "_datasets": [ { "name": "Mlifehist_ver1_0", "title": "Fisheries natural mortality example", "object": "Mlifehist_ver1_0", "file": "Mlifehist_ver1_0.rda", "class": [ "data.frame" ], "fields": [ "Order", "Family", "Genus", "Species", "SubSpecies", "Sex", "M", "K", "Linf", "tmax", "Temp" ], "rows": 230, "table": true, "tojson": true } ], "_help": [ { "page": "as_fitted_DAG", "title": "Convert phylosem to phylopath output", "topics": [ "as_fitted_DAG" ] }, { "page": "as_phylo4d", "title": "Convert phylosem to phylo4d", "topics": [ "as_phylo4d" ] }, { "page": "as_sem", "title": "Convert phylosem to sem output", "topics": [ "as_sem" ] }, { "page": "average", "title": "Choose model", "topics": [ "average" ] }, { "page": "average.compare_phylosem", "title": "Choose model", "topics": [ "average.compare_phylosem" ] }, { "page": "best", "title": "Extract best fitted model", "topics": [ "best" ] }, { "page": "best.compare_phylosem", "title": "Extract best fitted model", "topics": [ "best.compare_phylosem" ] }, { "page": "choice", "title": "Choose model", "topics": [ "choice" ] }, { "page": "choice.compare_phylosem", "title": "Choose model", "topics": [ "choice.compare_phylosem" ] }, { "page": "coef.phylosem", "title": "Extract path coefficients", "topics": [ "coef.phylosem" ] }, { "page": "compare_phylosem", "title": "Compare phylogenetic structural equation models", "topics": [ "compare_phylosem" ] }, { "page": "list_parameters", "title": "List fixed and random effects", "topics": [ "list_parameters" ] }, { "page": "Mlifehist_ver1_0", "title": "Fisheries natural mortality example", "topics": [ "Mlifehist_ver1_0" ] }, { "page": "parse_path", "title": "Parse path", "topics": [ "parse_path" ] }, { "page": "phylosem", "title": "Fit phylogenetic structural equation model", "topics": [ "phylosem" ] }, { "page": "phylosem_control", "title": "Detailed control for phylosem structure", "topics": [ "phylosem_control" ] }, { "page": "print.phylosem", "title": "Print parameter estimates and standard errors.", "topics": [ "print.phylosem" ] }, { "page": "summary.phylosem", "title": "summarize phylosem", "topics": [ "summary.phylosem" ] }, { "page": "vcov.phylosem", "title": "Extract Variance-Covariance Matrix", "topics": [ "vcov.phylosem" ] } ], "_readme": "https://github.com/James-Thorson-NOAA/phylosem/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "ape", "arm", "askpass", "base64enc", "BiocGenerics", "BiocManager", "boot", "cachem", "cli", "coda", "codetools", "cpp11", "crayon", "curl", "digest", "dplyr", "farver", "fastmap", "future", "future.apply", "generics", "ggforce", "ggm", "ggplot2", "ggraph", "ggrepel", "globals", "glue", "graph", "graphlayouts", "gridExtra", "gtable", "hms", "httr", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "listenv", "lme4", "magrittr", "MASS", "Matrix", "memoise", "mi", "mime", "minqa", "nlme", "nloptr", "openssl", "parallelly", "phylobase", "phylolm", "phylopath", "pillar", "pixmap", "pkgconfig", "plyr", "polyclip", "prettyunits", "progress", "purrr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rncl", "RNeXML", "S7", "scales", "sem", "sp", "stringi", "stringr", "sys", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "TMB", "tweenr", "utf8", "uuid", "vctrs", "viridis", "viridisLite", "withr", "XML", "xml2" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "comparison.Rmd", "filename": "comparison.html", "title": "Comparison with other packages", "author": "James T. Thorson and Wouter van der Bijl", "engine": "knitr::rmarkdown", "headings": [ "Comparison with phylolm", "Generalized linear models", "Poisson-distributed response", "Binomial regression", "Summary of PGLM results", "Compare with phylopath", "Comparison with sem", "Comparison with Rphylopars" ], "created": "2023-01-27 21:59:42", "modified": "2024-02-01 19:28:08", "commits": 17 }, { "source": "demonstration.Rmd", "filename": "demonstration.html", "title": "Demonstration of selected features", "author": "James T. Thorson", "engine": "knitr::rmarkdown", "headings": [ "Estimability for multiple covariance transformations", "Scaling of runtime with increased tree size" ], "created": "2023-06-13 22:29:14", "modified": "2024-02-01 19:28:08", "commits": 8 }, { "source": "phylopath.Rmd", "filename": "phylopath.html", "title": "Detailed comparison with phylopath", "author": "Wouter van der Bijl", "engine": "knitr::rmarkdown", "headings": [ "Model comparison: some important differences", "Model fitting: sometimes different" ], "created": "2023-02-03 15:38:17", "modified": "2024-02-01 19:28:08", "commits": 9 }, { "source": "fisheries.Rmd", "filename": "fisheries.html", "title": "Phylogenetic comparative methods in fisheries science", "author": "James T. Thorson", "engine": "knitr::rmarkdown", "headings": [ "Preparing the Then et al. mortality database", "Fitting and selecting among phylogenetic structural equation models", "Visualizing output", "Sensitivity to using taxonomic tree" ], "created": "2023-10-07 04:45:58", "modified": "2024-02-01 19:28:08", "commits": 4 } ], "_score": 4.643452676486188, "_indexed": false, "_nocasepkg": "phylosem", "_universes": [ "noaa-fisheries-integrated-toolbox" ], "_indexurl": "https://james-thorson-noaa.r-universe.dev/phylosem", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.4", "date": "2026-07-16T06:34:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/e8c224649e1e4d7f7364787daf22d627ecb2a13f972b3fb3119c2b5596a59b53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.7.0", "os": "linux", "version": "1.1.4", "date": "2026-07-16T06:35:11.000Z", "distro": "resolute", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/6e048676f5aa828f0880591ca1c08b5b0debd6654c399d331ee0bae589dc13f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.6.1", "os": "linux", "version": "1.1.4", "date": "2026-07-16T06:34:45.000Z", "distro": "resolute", "arch": "aarch64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/0aadb41f2e9a261cd75536541c4476e268b3ea132f2734da5ba5b9b538b54e9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.6.1", "os": "linux", "version": "1.1.4", "date": "2026-07-16T06:34:19.000Z", "distro": "resolute", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/3c86ecba20f6cd04aa1e5de86d058adccac479582f1e77adb5ecc89567b059f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.5.3", "os": "mac", "version": "1.1.4", "date": "2026-07-16T06:32:13.000Z", "arch": "aarch64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/679f96fd593d0ca0c452a2de939a3ee2933c010afab377c401614b70fd19fc73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.5.3", "os": "mac", "version": "1.1.4", "date": "2026-07-16T06:35:45.000Z", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/57378f1de503fe2db8d67a3495f9be466643bfbfb57b1c94e7ee382d03e5bfc2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.6.1", "os": "mac", "version": "1.1.4", "date": "2026-07-16T06:32:24.000Z", "arch": "aarch64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/8333592a99eec966a37d56eab3558c006043ada8930d4e54fa3308e135162239", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.6.1", "os": "mac", "version": "1.1.4", "date": "2026-07-16T06:33:50.000Z", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/7f28eddd45d23ea92bda52803e4824e2f3b3cec561a836db1379178d0dc86a99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.7.0", "os": "win", "version": "1.1.4", "date": "2026-07-16T06:32:46.000Z", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/da2e910215da955720c116cd5537d7248893c87c8b3d5259955eb9e015092450", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.5.3", "os": "win", "version": "1.1.4", "date": "2026-07-16T06:32:30.000Z", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/721729c71dda2ee17c18dec2104af80e1c9742efc20a2c8f739717de5a142f88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" }, { "r": "4.6.1", "os": "win", "version": "1.1.4", "date": "2026-07-16T06:32:35.000Z", "arch": "x86_64", "commit": "321fc949e6fcde4a93c112d004afda997c636504", "fileid": "https://r2.ropensci.org/4a4f490aad1567fe95667438264ca54ee11c5af5b2d0de87bea4c418b7ffddb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/29476287564" } ] }