{ "_id": "6adb6a9bad718eea59ecbdfd", "Package": "ccva", "Type": "Package", "Title": "Climate Change Vulnerability Assessment with Constrained Latent\nModels", "Version": "0.1.1", "Authors@R": "person(\"Hassan\", \"Doosti\", email = \"hassan.doosti@mq.edu.au\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(affiliation = \"Macquarie University\"))", "Description": "A general framework for climate change vulnerability\nassessment (CCVA) of any species and any dataset. Variables are\ntagged as exposure, sensitivity or adaptive capacity; each\ncomponent is computed from its own predictors by a chosen\nmethod; and the three components are combined into\nvulnerability. Methods range from the rule-based framework of\nFoden et al. (2013) and the\nconventional weighted index of Ofori et al. (2017)\n to shape-constrained additive\nmodels ('scam'), latent-variable structural equation models\n('lavaan') in which vulnerability is inferred from observable\nproxies, and penalised regression ('glmnet') for\nhigh-dimensional predictors. Missing traits and outcomes are\nhandled by full-information maximum likelihood. Ecological\nknowledge enters as explicit constraints on predictors, on each\ncomponent's role and on the links between components.\nDiagnostics, validation against observed outcomes, bootstrap\nand weight-based uncertainty, calibrated risk predictions and\nplots for every step are included.", "License": "GPL (>= 3)", "URL": "https://github.com/DoostiH/ccva", "BugReports": "https://github.com/DoostiH/ccva/issues", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "RoxygenNote": "7.3.1", "Repository": "https://doostih.r-universe.dev", "Date/Publication": "2026-10-23 04:18:15 UTC", "RemoteUrl": "https://github.com/doostih/ccva", "RemoteRef": "HEAD", "RemoteSha": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 13:50:07 UTC", "User": "root" }, "Author": "Hassan Doosti [aut, cre, cph] (affiliation: Macquarie University)", "Maintainer": "Hassan Doosti ", "_user": "doostih", "_type": "src", "_file": "ccva_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/fe555569771becc99db10fecb3be0607b4f5224961f478bf86b638bf02694e23", "_filesize": 2535652, "_sha256": "fe555569771becc99db10fecb3be0607b4f5224961f478bf86b638bf02694e23", "_expires": "2027-01-31T14:09:29.000Z", "_created": "2026-10-23T13:50:07.000Z", "_published": "2026-10-23T14:09:31.508Z", "_upstream": "https://github.com/doostih/ccva", "_status": "success", "_maintainer": { "name": "Hassan Doosti", "email": "hassan.doosti@mq.edu.au" }, "_jobs": [ { "job": 120450837292, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12506721537" }, { "job": 120450837084, "time": 181, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12507000293" }, { "job": 120450837093, "time": 162, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12506553632" }, { "job": 120450837228, "time": 104, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12507735682" }, { "job": 120446731595, "time": 513, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12506191594" }, { "job": 120450837288, "time": 95, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12506312747" }, { "job": 120450837331, "time": 99, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12507120188" }, { "job": 120450837181, "time": 132, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12505858747" }, { "job": 120450837073, "time": 135, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12506820877" } ], "_buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225", "_commit": { "id": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "author": "DoostiH <165978949+DoostiH@users.noreply.github.com>", "committer": "DoostiH <165978949+DoostiH@users.noreply.github.com>", "message": "Release 0.1.1 with cross-validation and cluster bootstrap\n", "time": 1792729095 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "lavaan", "version": ">= 0.6-12", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "scam", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "doostih", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-42", "n": 8 }, { "week": "2026-43", "n": 2 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "doostih", "count": 6, "uuid": 165978949 } ], "_userbio": { "uuid": 165978949, "type": "user", "name": "DoostiH", "followers": 0 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ccva" }, "_devurl": "https://github.com/doostih/ccva", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/ccva.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/doostih/ccva", "_realowner": "doostih", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2026-10-22" } ], "_exports": [ "as_ccva", "ccva", "ccva_adaptive", "ccva_adjust_method", "ccva_aggregate", "ccva_calibrate", "ccva_check", "ccva_classify", "ccva_colours", "ccva_combine", "ccva_compare", "ccva_component", "ccva_constraints", "ccva_cv", "ccva_default_constraints", "ccva_exposure", "ccva_methods", "ccva_plot", "ccva_rank", "ccva_recommend", "ccva_register", "ccva_report", "ccva_sdm_exposure", "ccva_sensitivity", "ccva_sim_data", "ccva_simulate", "ccva_thermal_margin", "ccva_uncertainty", "ccva_unconstrained", "ccva_unregister", "ccva_validate", "constrain_bounds", "constrain_equal", "constrain_fixed", "constrain_link", "constrain_moderator", "constrain_shape", "constrain_sign", "theme_ccva" ], "_datasets": [ { "name": "ccva_sim", "title": "Simulated CCVA dataset", "object": "ccva_sim", "class": [ "data.frame" ], "fields": [ "species", "E1_risk", "E2_risk", "E3_risk", "s1_thermal", "s2_range", "s3_climzones", "s4_habitat", "s5_diet", "s6_reprorate", "s7_repromode", "s8_clutch", "s9_survival", "s10_genlen", "s11_lifespan", "a1_genetic", "a2_bodysize", "a3_lowfrag", "a4_microhab", "iucn", "pop_trend", "range_change", "E_star", "S_star", "A_star", "V_star" ], "rows": 300, "table": true, "tojson": true } ], "_help": [ { "page": "as_ccva", "title": "Build a CCVA dataset", "topics": [ "as_ccva" ] }, { "page": "ccva", "title": "Run a complete CCVA", "topics": [ "ccva" ] }, { "page": "ccva_adjust_method", "title": "Adjust trait measurements for assay methodology", "topics": [ "ccva_adjust_method" ] }, { "page": "ccva_aggregate", "title": "Aggregate species vulnerability to sites or communities", "topics": [ "ccva_aggregate" ] }, { "page": "ccva_calibrate", "title": "Calibrated risk predictions", "topics": [ "ccva_calibrate" ] }, { "page": "ccva_check", "title": "Diagnose the indicators before combining them", "topics": [ "ccva_check" ] }, { "page": "ccva_classify", "title": "Classify vulnerability scores into Low / Moderate / High", "topics": [ "ccva_classify" ] }, { "page": "ccva_combine", "title": "Combine the components into vulnerability", "topics": [ "ccva_combine" ] }, { "page": "ccva_compare", "title": "Compare several CCVA fits", "topics": [ "ccva_compare" ] }, { "page": "ccva_component", "title": "Score the exposure, sensitivity and adaptive-capacity components", "topics": [ "ccva_adaptive", "ccva_component", "ccva_exposure", "ccva_sensitivity" ] }, { "page": "ccva_constraints", "title": "Constraints on predictors and components", "topics": [ "ccva_constraints", "ccva_default_constraints", "ccva_unconstrained", "constrain_bounds", "constrain_equal", "constrain_fixed", "constrain_link", "constrain_moderator", "constrain_shape", "constrain_sign" ] }, { "page": "ccva_cv", "title": "Cross-validated vulnerability scores", "topics": [ "ccva_cv" ] }, { "page": "ccva_methods", "title": "List available methods", "topics": [ "ccva_methods" ] }, { "page": "ccva_plot", "title": "Plot any step of a CCVA", "topics": [ "ccva_plot" ] }, { "page": "ccva_rank", "title": "Rank units by vulnerability", "topics": [ "ccva_rank" ] }, { "page": "ccva_recommend", "title": "Match methods to the data available", "topics": [ "ccva_recommend" ] }, { "page": "ccva_register", "title": "Register a new component or combination method", "topics": [ "ccva_register", "ccva_unregister" ] }, { "page": "ccva_report", "title": "Write a reproducible CCVA report", "topics": [ "ccva_report" ] }, { "page": "ccva_sdm_exposure", "title": "Compute exposure predictors from species distribution model output", "topics": [ "ccva_sdm_exposure" ] }, { "page": "ccva_sim", "title": "Simulated CCVA dataset", "topics": [ "ccva_sim" ] }, { "page": "ccva_sim_data", "title": "Specification of the bundled simulated data", "topics": [ "ccva_sim_data" ] }, { "page": "ccva_simulate", "title": "Simulate CCVA data with a known latent structure", "topics": [ "ccva_simulate" ] }, { "page": "ccva_thermal_margin", "title": "Compute thermal sensitivity predictors", "topics": [ "ccva_thermal_margin" ] }, { "page": "ccva_uncertainty", "title": "Quantify uncertainty in vulnerability scores and rankings", "topics": [ "ccva_uncertainty" ] }, { "page": "ccva_validate", "title": "Validate vulnerability scores against observed outcomes", "topics": [ "ccva_validate" ] }, { "page": "predict.ccva_fit", "title": "Predict vulnerability for new units", "topics": [ "predict.ccva_fit" ] }, { "page": "theme_ccva", "title": "Colours and theme used by ccva plots", "topics": [ "ccva_colours", "theme_ccva" ] } ], "_readme": "https://github.com/doostih/ccva/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lavaan", "lifecycle", "MASS", "mnormt", "numDeriv", "pbivnorm", "quadprog", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "framework.Rmd", "filename": "framework.html", "title": "A statistical CCVA workflow, step by step", "engine": "knitr::rmarkdown", "headings": [ "1. Match the method to the data", "2. Control sensitivity traits for methodology", "3. Test how well the data measure E, S and A", "Incomplete trait data", "Rule-based assessments", "4. Make the causal hypotheses explicit", "5. Shapes that ecology justifies", "6. From rankings to calibrated risk", "7. Spatial prioritisation", "What is not (yet) in the package", "Reference" ], "created": "2026-10-14 05:09:46", "modified": "2026-10-23 04:18:15", "commits": 3 }, { "source": "ccva.Rmd", "filename": "ccva.html", "title": "Climate change vulnerability assessment with ccva", "engine": "knitr::rmarkdown", "headings": [ "1. Data", "Before combining anything: diagnostics", "2. The conventional baseline: Ofori et al. (2017)", "3. Vulnerability as a latent variable", "Which method recovers the truth?", "4. Constraints: imposing ecological knowledge", "When do constraints matter?", "Adaptive capacity as a moderator", "5. High-dimensional predictors", "6. How certain is the ranking?", "7. Classification and outputs", "8. Extending the framework", "References" ], "created": "2026-10-14 03:36:49", "modified": "2026-10-14 03:36:49", "commits": 1 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "ccva", "_universes": [ "doostih" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-10-23T13:53:57.000Z", "distro": "resolute", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/f3dbee4327d8eb69d35624a87402019e3ffca36f52ec029a23de38200f1fa4a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-10-23T13:53:59.000Z", "distro": "resolute", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/f448cf6e01c66c1ee67f9046e46028c9a2973224263b4e92fa30dd336f5a61c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-10-23T14:08:05.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/eca9f1addae8cfbed72653260d75350d0e2cfccd9b8f0735a15160322eb59d23", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.6.1", "os": "mac", "version": "0.1.1", "date": "2026-10-23T14:07:36.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/5a4bc92b4081389122da56f39f32d8be9f905c8609d4c7ad69c62677a96add24", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-10-23T13:53:51.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/1006ee13ab15ddff7715e88c99c1f01269b88fa2a1d99f27916c9a9895b4ee7a", "status": "success", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-10-23T13:53:09.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/50e3a9486868cc9777bbce426f6c4792972241ac8f13ed007b0a555601dceb75", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-10-23T13:53:16.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/58455893dbfb094a881260c1a0f67c3811380fa3ddcc461848478c535274fcf7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-10-23T13:53:03.000Z", "commit": "2101cc5cbcb7898d23a64db3f37cb763a3fb698a", "fileid": "https://r2.ropensci.org/90dc5793956ba3b602378397bba8fa4739cc58c856fa3dd1a3b9f092efce45fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/doostih/actions/runs/39963304225" } ] }