{ "_id": "6ad6fc94d556c3a3418a647f", "Package": "crywolf", "Title": "Bayesian False-Positive Occupancy Models with Calibration Checks", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Diogo B.\", \"Provete\", email = \"dbprovete@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0097-0651\")),\nperson(\"Tessa\", \"Rhinehart\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4352-3464\")),\nperson(\"Liliana\", \"Piatti\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-6324-1723\")),\nperson(\"Larissa Sayuri Moreira\", \"Sugai\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6248-291X\"))\n)", "Description": "Fits single-season occupancy models that correct for false\npositives from automated detectors, such as acoustic\nclassifiers, using the multiple-methods (site-confirmation)\ndesign of Miller et al. (2011) , in\nwhich a subset of detections is verified. Models are written in\n'Stan' and fitted through 'cmdstanr'. The false-positive rate\ncan be constant or depend on site covariates, and the\ntrue-detection process accepts observation covariates and a\nrecorder random effect. The package also simulates data under\nhomogeneous, unstructured, and structured false-positive\nregimes and runs simulation-based calibration checks, so users\ncan ask whether the correction keeps nominal interval coverage\nfor their own design and how much verification it needs.", "License": "GPL (>= 3)", "URL": "https://github.com/diogoprov/crywolf,\nhttps://provetelab.org/crywolf/", "BugReports": "https://github.com/diogoprov/crywolf/issues", "VignetteBuilder": "knitr", "Remotes": [ "stan-dev/cmdstanr" ], "Additional_repositories": "https://stan-dev.r-universe.dev", "SystemRequirements": "CmdStan (>= 2.34;\nhttps://mc-stan.org/users/interfaces/cmdstan)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.1", "LazyData": "true", "Repository": "https://diogoprov.r-universe.dev", "Date/Publication": "2026-10-20 03:12:13 UTC", "RemoteUrl": "https://github.com/diogoprov/crywolf", "RemoteRef": "HEAD", "RemoteSha": "397d057b2301757044c53ea834919ce4ccc20d37", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-20 05:26:57 UTC", "User": "root" }, "Author": "Diogo B. Provete [aut, cre] (ORCID:\n),\nTessa Rhinehart [aut] (ORCID: ),\nLiliana Piatti [aut] (ORCID: ),\nLarissa Sayuri Moreira Sugai [aut] (ORCID:\n)", "Maintainer": "Diogo B. Provete ", "_user": "diogoprov", "_type": "src", "_file": "crywolf_1.3.0.tar.gz", "_fileid": "https://r2.ropensci.org/83ee169bb70aaaef8e49aed9c36e5d0febcb06500698379aeae34a915831f6d9", "_filesize": 4474422, "_sha256": "83ee169bb70aaaef8e49aed9c36e5d0febcb06500698379aeae34a915831f6d9", "_expires": "2027-01-28T05:30:57.000Z", "_created": "2026-10-20T05:26:57.000Z", "_published": "2026-10-20T05:30:59.839Z", "_upstream": "https://github.com/diogoprov/crywolf", "_status": "success", "_maintainer": { "name": "Diogo B. Provete", "email": "dbprovete@gmail.com", "login": "diogoprov", "bluesky": "@provete.bsky.social", "linkedin": "in/diogo-b-provete-phd-6a1673239", "orcid": "0000-0002-0097-0651", "description": "I'm a Deputy Editor - Ecology working at Wiley. I'm interested on metacommunity, macroevolution, and phylogenetic comparative methods of vertebrates", "uuid": 5214836 }, "_jobs": [ { "job": 118471020624, "time": 192, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12243401588" }, { "job": 118471020711, "time": 167, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12243326701" }, { "job": 118471020643, "time": 116, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12243486100" }, { "job": 118471020651, "time": 100, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12242952511" }, { "job": 118466987453, "time": 861, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12242489099" }, { "job": 118471020646, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12243236951" }, { "job": 118471020761, "time": 69, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12243550147" }, { "job": 118471020806, "time": 82, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12242533946" }, { "job": 118471020690, "time": 94, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12243236773" } ], "_buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726", "_commit": { "id": "397d057b2301757044c53ea834919ce4ccc20d37", "author": "diogoprov ", "committer": "diogoprov ", "message": "NEWS 1.3.0: tabela de ganhos por desenho, do benchmark reproduzível\n\nCo-Authored-By: Claude Fable 5.1 \n", "time": 1792465933 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "cmdstanr", "version": ">= 0.8.0", "role": "Imports" }, { "package": "loo", "role": "Imports" }, { "package": "posterior", "role": "Imports" }, { "package": "purrr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "bayesplot", "role": "Suggests" }, { "package": "furrr", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "progressr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "unmarked", "role": "Suggests" } ], "_owner": "diogoprov", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-42", "n": 26 }, { "week": "2026-43", "n": 3 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-10-15" }, { "name": "v1.1.0", "date": "2026-10-15" }, { "name": "v1.2.0", "date": "2026-10-16" }, { "name": "v1.3.0", "date": "2026-10-20" } ], "_stars": 0, "_contributors": [ { "user": "diogoprov", "count": 29, "uuid": 5214836 } ], "_userbio": { "uuid": 5214836, "type": "user", "name": "Dr. Diogo B. Provete", "followers": 45, "description": "I'm a Deputy Editor - Ecology working at Wiley. I'm interested on metacommunity, macroevolution, and phylogenetic comparative methods of vertebrates" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/crywolf" }, "_devurl": "https://github.com/diogoprov/crywolf", "_pkgdown": "https://provetelab.org/crywolf/", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/crywolf.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "as_draws_df", "fp_calibrate", "fp_calibrate_fit", "fp_compile", "fp_data", "fp_data_wide", "fp_occu", "fp_ppc", "fp_priors", "fp_stan_file", "fp_verification_curve", "loo", "simulate_fp" ], "_datasets": [ { "name": "curiango", "title": "Passive acoustic monitoring of the Common Pauraque in the Pantanal", "object": "curiango", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "curiango", "title": "Passive acoustic monitoring of the Common Pauraque in the Pantanal", "topics": [ "curiango" ] }, { "page": "fp_calibrate", "title": "Simulation-based calibration check for a study design", "topics": [ "fp_calibrate" ] }, { "page": "fp_calibrate_fit", "title": "Calibration of a fitted model on data like the real ones", "topics": [ "fp_calibrate_fit" ] }, { "page": "fp_compile", "title": "Compile (or load) the Stan model", "topics": [ "fp_compile" ] }, { "page": "fp_data", "title": "Assemble data for a false-positive occupancy model", "topics": [ "fp_data" ] }, { "page": "fp_data_wide", "title": "Assemble data from detection matrices", "topics": [ "fp_data_wide" ] }, { "page": "fp_occu", "title": "Fit a Bayesian false-positive occupancy model", "topics": [ "fp_occu" ] }, { "page": "fp_occu-methods", "title": "Methods for fp_occu fits", "topics": [ "as_draws_df.fp_occu", "coef.fp_occu", "fp_occu-methods", "loo.fp_occu", "predict.fp_occu", "print.fp_occu", "print.summary.fp_occu", "summary.fp_occu" ] }, { "page": "fp_ppc", "title": "Posterior predictive check for a false-positive occupancy model", "topics": [ "fp_ppc" ] }, { "page": "fp_priors", "title": "Prior settings for fp_occu()", "topics": [ "fp_priors" ] }, { "page": "fp_stan_file", "title": "Path to the Stan program", "topics": [ "fp_stan_file" ] }, { "page": "fp_verification_curve", "title": "Coverage as a function of verification effort", "topics": [ "fp_verification_curve" ] }, { "page": "plot.fp_calibration", "title": "Plot the results of a calibration check", "topics": [ "plot.fp_calibration" ] }, { "page": "simulate_fp", "title": "Simulate data for a false-positive occupancy model", "topics": [ "simulate_fp" ] }, { "page": "simulate.fp_occu", "title": "Simulate data from a fitted model", "topics": [ "simulate.fp_occu" ] } ], "_pkglogo": "https://github.com/diogoprov/crywolf/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/diogoprov/crywolf/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "checkmate", "cli", "cmdstanr", "data.table", "distributional", "generics", "glue", "jsonlite", "lifecycle", "loo", "magrittr", "matrixStats", "numDeriv", "pillar", "pkgconfig", "posterior", "processx", "ps", "purrr", "R6", "rlang", "tensorA", "tibble", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "curiango.Rmd", "filename": "curiango.html", "title": "Case study: the Common Pauraque in the Pantanal", "engine": "knitr::rmarkdown", "headings": [ "The data", "Fitting", "Convergence", "How often does each classifier err?", "Occupancy with and without false positives", "Does the false-positive rate track the environment?", "Model comparison", "Posterior predictive checks", "Predicted occupancy", "References" ], "created": "2026-10-15 02:44:05", "modified": "2026-10-15 11:22:46", "commits": 3 }, { "source": "calibration.Rmd", "filename": "calibration.html", "title": "Checking calibration and how much to verify", "engine": "knitr::rmarkdown", "headings": [ "The workflow", "How much to verify", "What to expect", "Calibrating a fitted model", "Plotting" ], "created": "2026-10-14 21:09:21", "modified": "2026-10-16 01:35:19", "commits": 7 }, { "source": "unmarked.Rmd", "filename": "unmarked.html", "title": "Coming from unmarked::occuFP()", "engine": "knitr::rmarkdown", "headings": [ "The data layout", "The same model fitted both ways", "Formulas", "What crywolf adds", "Predictions", "References" ], "created": "2026-10-15 05:06:37", "modified": "2026-10-15 05:06:37", "commits": 1 }, { "source": "crywolf.Rmd", "filename": "crywolf.html", "title": "Introduction to crywolf", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Example data", "The multiple-methods design", "Simulated data", "Your own data", "The multiple-methods false-positive occupancy model", "Basic model description", "Parameter names", "Fitting the constant-rate model with fp_occu()", "Convergence and model adequacy", "Convergence", "Posterior predictive check", "Modelling the false-positive rate", "Why the occupancy slope is biased", "A false-positive rate that tracks the occupancy covariate", "A false-positive rate that tracks the confusing gradient", "Sensitivity to the priors", "Variation that the covariates do not explain", "Model comparison with LOO", "Prediction", "Detection covariates and recorder effects", "The observation-confirmation design", "Next steps", "References" ], "created": "2026-10-14 21:09:21", "modified": "2026-10-16 02:21:58", "commits": 11 }, { "source": "simulation.Rmd", "filename": "simulation.html", "title": "Simulating false-positive regimes", "engine": "knitr::rmarkdown", "headings": [ "What a simulation returns", "Three false-positive regimes", "Homogeneous", "Unstructured", "Structured", "The observation process", "From one dataset to a calibration check", "References" ], "created": "2026-10-15 05:06:37", "modified": "2026-10-16 02:21:58", "commits": 3 }, { "source": "stan_model.Rmd", "filename": "stan_model.html", "title": "The Stan model", "engine": "knitr::rmarkdown", "headings": [ "Data", "Binomial rows", "Parameters", "Likelihood", "Parallel likelihood", "Priors and model block", "Generated quantities", "Modifying a copy", "References" ], "created": "2026-10-15 05:06:37", "modified": "2026-10-20 03:12:13", "commits": 5 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "crywolf", "_universes": [ "diogoprov" ], "_previous": "1.2.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-10-20T05:30:13.000Z", "distro": "resolute", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/1029f1ba9c281719eaf63fb7cfc61912204c86d7bcafb32b3f98ccf0a5d080c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.6.1", "os": "linux", "version": "1.3.0", "date": "2026-10-20T05:29:46.000Z", "distro": "resolute", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/ba92e9cac0dec0cffc63c1042cb1fcb27f29fbb6d25902641409d3dd500943e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-10-20T05:29:00.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/3fe9ef065799fe4adfbd4b97145046308296c334a251749cb77f1878f887b56c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.6.1", "os": "mac", "version": "1.3.0", "date": "2026-10-20T05:28:46.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/ebd9d51a1de49f2fbe0ff020a0591758a8d55a218680888ddddf8a426b66c54a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-10-20T05:30:00.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/605a8a6132151b95d8bc2a0def102c7b6cf034edcd346530a5600fbffa49476b", "status": "success", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-10-20T05:28:09.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/4c8158028d84054baf1ff49c330b3482dbd5dc34a57bda372e93048450f5757f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-10-20T05:28:15.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/c65d3cc439d42719ad9f63dce849c1d1a3c2b9a0e7b83f8ab3e3f4956de08d8f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" }, { "r": "4.6.1", "os": "win", "version": "1.3.0", "date": "2026-10-20T05:28:26.000Z", "commit": "397d057b2301757044c53ea834919ce4ccc20d37", "fileid": "https://r2.ropensci.org/fb76354bc6f380a795a08535957e7e656356e33656fa4b1ef524f146a99e4168", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/diogoprov/actions/runs/39373675726" } ] }