{ "_id": "6a1ed489b401979e7340e26d", "Package": "estar", "Title": "Ecological Stability Metrics", "Version": "1.0-1", "Authors@R": "c(\nperson(given = \"Ludmilla\",\nfamily = \"Figueiredo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ludmilla.figueiredo@protonmail.com\",\ncomment = c(ORCID = \"https://orcid.org/0000-0001-8217-7800\")),\nperson(given = \"Viktoriia\",\nfamily = \"Radchuk\",\nrole = c(\"aut\"),\nemail = \"radchuk@izw-berlin.de\",\ncomment = c(ORCID = \"https://orcid.org/0000-0003-3072-0095\")),\nperson(given = \"Cédric\",\nfamily = \"Scherer\",\nrole = c(\"ctb\"),\nemail = \"cedricphilippscherer@gmail.com\",\ncomment = c(ORCID = \"https://orcid.org/0000-0003-0465-2543\")))", "Description": "Standardises and facilitates the use of eleven established\nstability properties that have been used to assess systems’\nresponses to press or pulse disturbances at different\necological levels (e.g. population, community). There are two\nsets of functions. The first set corresponds to functions that\nmeasure stability at any level of organisation, from individual\nto community and can be applied to a time series of a system’s\nstate variables (e.g., body mass, population abundance, or\nspecies diversity). The properties included in this set are:\ninvariability, resistance, extent and rate of recovery,\npersistence, and overall ecological vulnerability. The second\nset of functions can be applied to Jacobian matrices. The\nfunctions in this set measure the stability of a community at\nshort and long time scales. In the short term, the community’s\nresponse is measured by maximal amplification, reactivity and\ninitial resilience (i.e. initial rate of return to\nequilibrium). In the long term, stability can be measured as\nasymptotic resilience and intrinsic stochastic invariability.\nFigueiredo et al. (2025) .", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Repository": "https://ludmillafigueiredo.r-universe.dev", "Date/Publication": "2026-05-20 13:54:44 UTC", "RemoteUrl": "https://github.com/ludmillafigueiredo/estar", "RemoteRef": "HEAD", "RemoteSha": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 14:21:58 UTC", "User": "root" }, "Author": "Ludmilla Figueiredo [aut, cre] (ORCID:\n),\nViktoriia Radchuk [aut] (ORCID:\n),\nCédric Scherer [ctb] (ORCID: )", "Maintainer": "Ludmilla Figueiredo ", "MD5sum": "d4f3ca6d75e318a3875e7bf76220a02f", "_user": "ludmillafigueiredo", "_type": "src", "_file": "estar_1.0-1.tar.gz", "_fileid": "0cb2dabff339a79fc6e3b3583fefce9a0ed715baf9528cbb9f535c1f92f8a908", "_filesize": 5239583, "_sha256": "0cb2dabff339a79fc6e3b3583fefce9a0ed715baf9528cbb9f535c1f92f8a908", "_created": "2026-05-20T14:21:58.000Z", "_published": "2026-06-02T13:03:05.858Z", "_distro": "noble", "_jobs": [ { "job": 79076474314, "time": 160, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7112727120" }, { "job": 79076474284, "time": 157, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7112725621" }, { "job": 79076474334, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7112729920" }, { "job": 79076474128, "time": 131, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7112706645" }, { "job": 79076473329, "time": 444, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7112656377" }, { "job": 79076473419, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358388093" }, { "job": 79076474129, "time": 126, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7112713254" }, { "job": 79076474155, "time": 116, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7112708513" }, { "job": 79076474159, "time": 99, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7112701327" } ], "_buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ludmillafigueiredo/estar", "_commit": { "id": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "author": "Ludmilla Figueiredo ", "committer": "Ludmilla Figueiredo ", "message": "set up rhub checks\n", "time": 1779285284 }, "_maintainer": { "name": "Ludmilla Figueiredo", "email": "ludmilla.figueiredo@protonmail.com", "login": "ludmillafigueiredo", "orcid": "0000-0001-8217-7800", "description": "Data and Code curator. #opensource", "uuid": 10743518 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "hesim", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "utils", "role": "Suggests" }, { "package": "MARSS", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" } ], "_owner": "ludmillafigueiredo", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-21", "n": 2 }, { "week": "2025-34", "n": 6 }, { "week": "2025-39", "n": 6 }, { "week": "2025-40", "n": 5 }, { "week": "2025-41", "n": 1 }, { "week": "2025-45", "n": 8 }, { "week": "2025-46", "n": 1 }, { "week": "2025-47", "n": 4 }, { "week": "2025-48", "n": 2 }, { "week": "2026-12", "n": 4 }, { "week": "2026-13", "n": 1 }, { "week": "2026-14", "n": 2 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-21", "n": 7 } ], "_tags": [ { "name": "1.0-0", "date": "2025-11-22" } ], "_stars": 2, "_contributors": [ { "user": "ludmillafigueiredo", "count": 265, "uuid": 10743518 }, { "user": "radchukv", "count": 59, "uuid": 40353544 }, { "user": "z3tt", "count": 8, "uuid": 7523556 } ], "_userbio": { "uuid": 10743518, "type": "user", "name": "Ludmilla Figueiredo", "description": "Data and Code curator. #opensource" }, "_downloads": { "count": 188, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/estar" }, "_devurl": "https://github.com/ludmillafigueiredo/estar", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/estar.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ludmillafigueiredo/estar", "_realowner": "ludmillafigueiredo", "_cranurl": true, "_releases": [ { "version": "1.0-0", "date": "2025-11-21" }, { "version": "1.0-1", "date": "2025-11-28" } ], "_exports": [ "asympt_resil", "extractB", "init_resil", "invariability", "max_amp", "oev", "persistence", "reactivity", "recovery_extent", "recovery_rate", "resistance", "stoch_var" ], "_datasets": [ { "name": "aquacomm_fgps", "title": "Macroinvertebrate aquatic community.", "object": "aquacomm_fgps", "class": [ "rowwise_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "time", "repli", "treat", "herb", "detr_herb", "carn", "omni", "detr" ], "rows": 192, "table": true, "tojson": true }, { "name": "aquacomm_resps", "title": "Macroinvertebrate aquatic community formatted for univariate metrics.", "object": "aquacomm_resps", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "time", "statvar_bl", "statvar_db" ], "rows": 16, "table": true, "tojson": true }, { "name": "comm_base", "title": "Macroinvertebrate aquatic community data formatted for calculation of compositional stability metrics", "object": "comm_base", "class": [ "data.frame" ], "fields": [ "time", "herb", "detr_herb", "carn", "omni", "detr" ], "rows": 16, "table": true, "tojson": true }, { "name": "comm_dist", "title": "Macroinvertebrate aquatic community data formatted for calculation of compositional stability metrics", "object": "comm_dist", "class": [ "data.frame" ], "fields": [ "time", "herb", "detr_herb", "carn", "omni", "detr" ], "rows": 16, "table": true, "tojson": true } ], "_help": [ { "page": "aquacomm_fgps", "title": "Macroinvertebrate aquatic community.", "topics": [ "aquacomm_fgps" ] }, { "page": "aquacomm_resps", "title": "Macroinvertebrate aquatic community formatted for univariate metrics.", "topics": [ "aquacomm_resps" ] }, { "page": "asympt_resil", "title": "Calculate the asymptotic resilience of a community after disturbance", "topics": [ "asympt_resil" ] }, { "page": "comm_base", "title": "Macroinvertebrate aquatic community data formatted for calculation of compositional stability metrics", "topics": [ "comm_base" ] }, { "page": "comm_dist", "title": "Macroinvertebrate aquatic community data formatted for calculation of compositional stability metrics", "topics": [ "comm_dist" ] }, { "page": "common_params", "title": "Define parameters that are common to all functions", "topics": [ "common_params" ] }, { "page": "extractB", "title": "Extract the community matrix (B)", "topics": [ "extractB" ] }, { "page": "init_resil", "title": "Calculate the initial resilience of a community after disturbance", "topics": [ "init_resil" ] }, { "page": "invariability", "title": "Calculate the invariability of a state variable after disturbance", "topics": [ "invariability" ] }, { "page": "max_amp", "title": "Calculate the maximal amplification of a community after disturbance", "topics": [ "max_amp" ] }, { "page": "oev", "title": "Calculate the overall ecological vulnerability of a community after disturbance", "topics": [ "oev" ] }, { "page": "persistence", "title": "Calculate the persistence of a state variable over a defined time interval", "topics": [ "persistence" ] }, { "page": "reactivity", "title": "Calculate the reactivity of a community after disturbance", "topics": [ "reactivity" ] }, { "page": "recovery_extent", "title": "Calculate the extent of recovery after disturbance", "topics": [ "recovery_extent" ] }, { "page": "recovery_rate", "title": "Calculate the rate of recovery after disturbance", "topics": [ "recovery_rate" ] }, { "page": "resistance", "title": "Calculate the resistance of a state variable to disturbance", "topics": [ "resistance" ] }, { "page": "stoch_var", "title": "Calculate the intrinsic stochastic invariability of a community from its community matrix.", "topics": [ "stoch_var" ] } ], "_readme": "https://github.com/ludmillafigueiredo/estar/raw/HEAD/README.md", "_rundeps": [ "cli", "cluster", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "MASS", "Matrix", "mgcv", "nlme", "permute", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "vegan", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "functional_stability_properties.Rmd", "filename": "functional_stability_properties.html", "title": "Functional stability properties", "engine": "knitr::rmarkdown", "headings": [ "Overview of the data", "Main functions", "Functional stability", "Invariability", "Resistance", "Rate of recovery", "Extent of recovery", "Persistence", "Overall Ecological Vulnerability", "Performance", "Recovery rate", "Recovery extent", "References" ], "created": "2025-11-26 15:15:08", "modified": "2026-05-20 13:49:41", "commits": 3 }, { "source": "jacobian_stability_properties.Rmd", "filename": "jacobian_stability_properties.html", "title": "Jacobian stability properties", "engine": "knitr::rmarkdown", "headings": [ "Overview of demonstration data", "MARSS models", "Introduction to MARSS models", "MARSS in estar", "Minimal case", "Reactivity", "Maximal amplification", "Initial resilience", "Asymptotic resilience", "Stochastic invariability", "Performance of functions", "References" ], "created": "2025-11-26 15:15:08", "modified": "2026-05-20 13:50:25", "commits": 5 } ], "_score": 5.8061799739838875, "_indexed": true, "_nocasepkg": "estar", "_universes": [ "ludmillafigueiredo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0-1", "date": "2026-05-20T14:24:34.000Z", "distro": "noble", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "228262ba612b6cad6b8c4765e90db7b99158b22e3eeed9b37f126afb9e95d242", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.6.0", "os": "linux", "version": "1.0-1", "date": "2026-05-20T14:24:31.000Z", "distro": "noble", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "77454396b704b7c2da96e38d27dfe87e328be3bb34f184cdfd25c20e04da09d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.5.3", "os": "mac", "version": "1.0-1", "date": "2026-05-20T14:24:50.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "6c633b3753100732cfd4e786badb5111ecae04e032b1eb8d016be9f4ff47e13b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.6.0", "os": "mac", "version": "1.0-1", "date": "2026-05-20T14:23:57.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "60245f8f4ba2c99cc1e26bf11351aa28902dee7c7a558780eb61756d7be2b4a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.7.0", "os": "win", "version": "1.0-1", "date": "2026-05-20T14:23:56.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "b7ebe217db468a39ab6b01d0757eb4bb604225ac041ab1ba1cd23ab96930ca02", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.5.3", "os": "win", "version": "1.0-1", "date": "2026-05-20T14:23:40.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "a0d012fa21dea4fc2047af40cb6f5f4619c2006f8606552cc1b2c84efa023b35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.6.0", "os": "win", "version": "1.0-1", "date": "2026-05-20T14:23:28.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "92c6937a1f2b78c5ba9e50ee892d357bc9b812f3f5669d31a653e7dd6ecd7a9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" }, { "r": "4.6.0", "os": "wasm", "version": "1.0-1", "date": "2026-06-02T13:01:52.000Z", "commit": "ac54552bf80e27d6b3e3758a1c90dc4fa4ad93b7", "fileid": "361c9691a57c7d0c0d3bea357d8e457fb13a1cbe17b92c59292298d67e4f983e", "status": "success", "buildurl": "https://github.com/r-universe/ludmillafigueiredo/actions/runs/26168341085" } ] }