{ "_id": "6a1b10b51d7bb097a0a0b6b5", "Package": "ecoregime", "Title": "Analysis of Ecological Dynamic Regimes", "Version": "0.3.0", "Authors@R": "person(given = \"Martina\", family = \"Sánchez-Pinillos\",\nemail = \"martina.sanchez.pinillos@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-1499-4507\"))", "Description": "A toolbox for implementing the Ecological Dynamic Regime\nframework (Sánchez-Pinillos et al., 2023\n) to characterize and compare groups of\necological trajectories in multidimensional spaces defined by\nstate variables. The package includes the RETRA-EDR algorithm\nto identify representative trajectories, functions to generate,\nsummarize, and visualize representative trajectories, and\nseveral metrics to quantify the distribution and heterogeneity\nof trajectories in an ecological dynamic regime and quantify\nthe dissimilarity between two or more ecological dynamic\nregimes. The package also includes a set of functions to assess\necological resilience based on ecological dynamic regimes\n(Sánchez-Pinillos et al., 2024\n).", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://mspinillos.github.io/ecoregime/,\nhttps://github.com/MSPinillos/ecoregime", "BugReports": "https://github.com/MSPinillos/ecoregime/issues", "LazyData": "true", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libx11-dev\nzlib1g-dev", "Repository": "https://mspinillos.r-universe.dev", "Date/Publication": "2026-05-30 14:46:45 UTC", "RemoteUrl": "https://github.com/mspinillos/ecoregime", "RemoteRef": "HEAD", "RemoteSha": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 16:17:31 UTC", "User": "root" }, "Author": "Martina Sánchez-Pinillos [aut, cre, cph] (ORCID:\n)", "Maintainer": "Martina Sánchez-Pinillos ", "MD5sum": "1c9876502624cbef1ab76463369e1181", "_user": "mspinillos", "_type": "src", "_file": "ecoregime_0.3.0.tar.gz", "_fileid": "a248b5d37809da2fef4abadac947eaa3395323508d815ce5408ec90613fb36ce", "_filesize": 2305998, "_sha256": "a248b5d37809da2fef4abadac947eaa3395323508d815ce5408ec90613fb36ce", "_created": "2026-05-30T16:17:31.000Z", "_published": "2026-05-30T16:30:45.275Z", "_distro": "noble", "_jobs": [ { "job": 78661334033, "time": 283, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7309588315" }, { "job": 78661334032, "time": 249, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7309584807" }, { "job": 78661334027, "time": 206, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309630518" }, { "job": 78661334030, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309637881" }, { "job": 78661105644, "time": 239, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7309558095" }, { "job": 78661334026, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7309572536" }, { "job": 78661334070, "time": 157, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7309574455" }, { "job": 78661334055, "time": 180, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7309576805" }, { "job": 78661334019, "time": 222, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7309581714" } ], "_buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mspinillos/ecoregime", "_commit": { "id": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "author": "Martina Sánchez-Pinillos ", "committer": "Martina Sánchez-Pinillos ", "message": "gitignore\n", "time": 1780152405 }, "_maintainer": { "name": "Martina Sánchez-Pinillos", "email": "martina.sanchez.pinillos@gmail.com", "orcid": "0000-0002-1499-4507" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "ecotraj", "version": ">= 1.1.1", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "shape", "role": "Imports" }, { "package": "smacof", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "plotrix", "role": "Suggests" }, { "package": "primer", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "vegan", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" } ], "_owner": "mspinillos", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-34", "n": 1 }, { "week": "2025-42", "n": 10 }, { "week": "2025-43", "n": 2 }, { "week": "2025-44", "n": 3 }, { "week": "2025-45", "n": 1 }, { "week": "2026-22", "n": 1 } ], "_tags": [ { "name": "v0.3.0", "date": "2025-10-29" } ], "_stars": 9, "_contributors": [ { "user": "mspinillos", "count": 282, "uuid": 27857581 } ], "_userbio": { "uuid": 27857581, "type": "user", "name": "Martina Sánchez-Pinillos", "description": "Postdoctoral researcher at UQAM. Interested in quantifying ecological resilience and assessing post-disturbance ecosystem dynamics." }, "_downloads": { "count": 170, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ecoregime" }, "_devurl": "https://github.com/mspinillos/ecoregime", "_pkgdown": "https://mspinillos.github.io/ecoregime/", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ecoregime.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mspinillos/ecoregime", "_realowner": "mspinillos", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2023-08-11" }, { "version": "0.1.3", "date": "2023-09-10" }, { "version": "0.2.0", "date": "2024-04-17" }, { "version": "0.2.1", "date": "2025-05-01" }, { "version": "0.3.0", "date": "2025-10-29" } ], "_exports": [ "amplitude", "dBD", "dDis", "define_retra", "dEve", "dist_edr", "net_change", "plot_edr", "recovery", "resistance", "retra_edr", "state_to_trajectory" ], "_datasets": [ { "name": "EDR_data", "title": "Ecological Dynamic Regime data", "object": "EDR_data", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "define_retra", "title": "Define representative trajectories from trajectory features", "topics": [ "define_retra" ] }, { "page": "deviation_metrics", "title": "Metrics of trajectory deviation with respect to a reference trajectory", "topics": [ "amplitude", "deviation_metrics", "net_change", "recovery", "resistance" ] }, { "page": "dist_edr", "title": "Dissimilarities between Ecological Dynamic Regimes", "topics": [ "dist_edr" ] }, { "page": "EDR_data", "title": "Ecological Dynamic Regime data", "topics": [ "EDR_data" ] }, { "page": "EDR_metrics", "title": "Metrics of Ecological Dynamic Regimes", "topics": [ "dBD", "dDis", "dEve", "EDR_metrics" ] }, { "page": "plot_edr", "title": "Plot Ecological Dynamic Regimes", "topics": [ "plot_edr" ] }, { "page": "plot.RETRA", "title": "Plot representative trajectories of Ecological Dynamic Regimes", "topics": [ "plot.RETRA" ] }, { "page": "retra_edr", "title": "Representative trajectories in Ecological Dynamic Regimes (RETRA-EDR)", "topics": [ "retra_edr" ] }, { "page": "state_to_trajectory", "title": "Position of a state with respect to a trajectory", "topics": [ "state_to_trajectory" ] }, { "page": "summary.RETRA", "title": "Summarize representative trajectories", "topics": [ "summary.RETRA" ] } ], "_pkglogo": "https://github.com/mspinillos/ecoregime/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/mspinillos/ecoregime/raw/HEAD/README.md", "_rundeps": [ "ape", "backports", "base64enc", "bit", "bit64", "boot", "broom", "bslib", "cachem", "checkmate", "class", "cli", "clipr", "cluster", "codetools", "colorspace", "cpp11", "crayon", "data.table", "digest", "doParallel", "dplyr", "e1071", "ecotraj", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "foreach", "foreign", "Formula", "fs", "gdata", "generics", "ggplot2", "glmnet", "glue", "gridExtra", "gtable", "gtools", "haven", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "isoband", "iterators", "jomo", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "memoise", "mice", "mime", "minqa", "mitml", "nlme", "nloptr", "nnet", "nnls", "numDeriv", "ordinal", "pan", "pillar", "pkgconfig", "plotrix", "polynom", "prettyunits", "progress", "proxy", "purrr", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "readr", "reformulas", "rlang", "rmarkdown", "rpart", "rstudioapi", "S7", "sass", "scales", "shape", "smacof", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "ucminf", "utf8", "vctrs", "viridisLite", "vroom", "weights", "withr", "wordcloud", "xfun", "yaml" ], "_vignettes": [ { "source": "EDR_framework.Rmd", "filename": "EDR_framework.html", "title": "Ecological Dynamic Regime framework", "author": "Martina Sánchez-Pinillos", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1.1. Ecological Dynamic Regimes and the EDR framework", "1.2. About this vignette", "2. Trajectory data, state and trajectory spaces", "3. Defining EDRs", "3.1. Identifying EDRs from clustering analyses", "3.2. Defining EDRs based on ecological properties", "4. Representative trajectories", "4.1. Identifying representative trajectories with RETRA-EDR", "4.2. Visualizing representative trajectories in the state space", "4.3. Defining representative trajectories based on trajectory features", "4.4. Variation of ecological properties along representative trajectories", "5. Distribution and heterogeneity of ecological trajectories in EDRs", "5.1. Dynamic dispersion (dDis)", "5.2. Dynamic beta diversity (dBD)", "5.3. Dynamic evenness (dEve)", "6. Comparing EDRs", "Acknowledgements" ], "created": "2023-01-01 10:54:13", "modified": "2025-10-27 10:06:29", "commits": 26 }, { "source": "Resilience.Rmd", "filename": "Resilience.html", "title": "Ecological resilience to pulse disturbances", "author": "Martina Sánchez-Pinillos", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1.1. Ecological resilience and the EDR framework", "1.2. About this vignette", "2. Assessing ecological dynamic regimes", "2.1. Identifying the reference ecological dynamic regime", "2.2. Define the main dynamic trends through representative trajectories", "3. Metrics of ecological resilience to pulse disturbances", "3.1. Resistance", "3.2. Amplitude", "3.3. Recovery", "3.4. Net change", "4. Assessing the ecological resilience of systems affected by pulse disturbances", "Acknowledgements" ], "created": "2024-04-04 21:47:17", "modified": "2024-04-06 22:39:52", "commits": 4 } ], "_score": 5.7737864449811935, "_indexed": true, "_nocasepkg": "ecoregime", "_universes": [ "mspinillos" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-05-30T16:20:45.000Z", "distro": "noble", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "a46da6b286cf422d1cd98d2adbe3ca9189d22e920d94108878852439c8a9a027", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.6.0", "os": "linux", "version": "0.3.0", "date": "2026-05-30T16:20:11.000Z", "distro": "noble", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "f0312e3d9a191a9bb546f43913c0ed009e2b51f29e2eb516f5ef12627c406b48", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-05-30T16:27:41.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "696f36ea7bb8fd520c21a293ccc6795dc5c59d592346a8307a8198e6f3a58744", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.6.0", "os": "mac", "version": "0.3.0", "date": "2026-05-30T16:28:32.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "4d2195d7b9b35f77ef6fb603d7d99337570bd2d951ec6e75b540e942e189dc6c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-05-30T16:20:10.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "92f65249239b3ad63e4374c259830eb57088c5b167bcf994e29f5c18bc46021c", "status": "success", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-05-30T16:19:13.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "9acdc7087bc653680a4d95f76122ff345c3ff8d75bd5e00b678e6dded3f9a3e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-05-30T16:19:07.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "ffb22b0fb04f1428ec509f3fc1123be4916393cbc85bc4dea49d6976452e9b3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" }, { "r": "4.6.0", "os": "win", "version": "0.3.0", "date": "2026-05-30T16:19:22.000Z", "commit": "d2f1d3dd9fe211d4a69ecc6e1bcae91bf82e99ad", "fileid": "fb18e23db09fef76fc9229db96d361886acc964b1f918f8e7f148560e1623a30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mspinillos/actions/runs/26688647435" } ] }