{ "_id": "6a12c5f6acfb0bcc41d1fba5", "Package": "Xcertainty", "Type": "Package", "Title": "Estimating Lengths and Uncertainty from Photogrammetric Imagery", "Version": "1.0.1", "Date": "2024-10-25", "Authors@R": "c(person(given = \"Joshua\",\nfamily = \"Hewitt\",\nrole = \"aut\"),\nperson(given = \"K.C.\",\nfamily = \"Bierlich\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bierlick@oregonstate.edu\"),\nperson(given = \"Enrico\",\nfamily = \"Pirotta\",\nrole = \"aut\"))", "Author": "Joshua Hewitt [aut], K.C. Bierlich [aut, cre], Enrico Pirotta\n[aut]", "Maintainer": "K.C. Bierlich ", "Description": "Implementation of Bayesian models for estimating object\nlengths and morphological relationships between object lengths\nusing photographic data collected from drones. The Bayesian\nmodel is described in \"Bayesian approach for predicting\nphotogrammetric uncertainty in morphometric measurements\nderived from drones\" (Bierlich et al., 2021,\n).", "URL": "https://github.com/MMI-CODEX/Xcertainty", "BugReports": "https://github.com/MMI-CODEX/Xcertainty/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr, rmarkdown", "LazyData": "true", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev", "Repository": "https://mmi-codex.r-universe.dev", "Date/Publication": "2025-05-28 16:35:52 UTC", "RemoteUrl": "https://github.com/mmi-codex/xcertainty", "RemoteRef": "HEAD", "RemoteSha": "8bddc787820681a6c01857667510922285328567", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 09:30:12 UTC", "User": "root" }, "MD5sum": "76acd5aaf826477493097bf1df6ac0d4", "_user": "mmi-codex", "_type": "src", "_file": "Xcertainty_1.0.1.tar.gz", "_fileid": "17e5fca1bf3352816ef5a4376ab1ab29258535dd64a6ecece03ce260b8c9c91f", "_filesize": 1468772, "_sha256": "17e5fca1bf3352816ef5a4376ab1ab29258535dd64a6ecece03ce260b8c9c91f", "_created": "2026-05-24T09:30:12.000Z", "_published": "2026-05-24T09:33:42.044Z", "_distro": "noble", "_jobs": [ { "job": 77587156775, "time": 178, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7184054659" }, { "job": 77587156784, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7184054354" }, { "job": 77587156791, "time": 145, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7184049320" }, { "job": 77587156778, "time": 155, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7184049531" }, { "job": 77586971257, "time": 199, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7184037111" }, { "job": 77587156785, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7184049395" }, { "job": 77587156787, "time": 134, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7184050467" }, { "job": 77587156788, "time": 135, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7184050955" }, { "job": 77587156789, "time": 105, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7184047919" } ], "_buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mmi-codex/xcertainty", "_commit": { "id": "8bddc787820681a6c01857667510922285328567", "author": "KC Bierlich <45541548+KCBierlich@users.noreply.github.com>", "committer": "GitHub ", "message": "Update Xcertainty.Rmd\n\ncorrected typo of \"calibration_data$...\" to \"whale_data$...\"", "time": 1748450152 }, "_maintainer": { "name": "K.C. Bierlich", "email": "bierlick@oregonstate.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.2", "role": "Depends" }, { "package": "nimble", "role": "Depends" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "ggdist", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" } ], "_owner": "mmi-codex", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-22", "n": 2 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "jmhewitt", "count": 32, "uuid": 6801172 }, { "user": "kcbierlich", "count": 31, "uuid": 45541548 } ], "_userbio": { "uuid": 180221108, "type": "organization", "name": "CODEX", "description": "The Marine Mammal Institute's Center of Drone Excellence (CODEX) at Oregon State University" }, "_downloads": { "count": 625, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Xcertainty" }, "_devurl": "https://github.com/mmi-codex/xcertainty", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/Xcertainty.html", "manual.pdf" ], "_homeurl": "https://github.com/mmi-codex/xcertainty", "_realowner": "mmi-codex", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2024-10-21" }, { "version": "1.0.1", "date": "2024-10-26" } ], "_exports": [ "body_condition", "breakFun", "calibration_sampler", "combine_observations", "growth_curve_sampler", "independent_length_sampler", "nondecreasing_length_sampler", "parse_observations" ], "_datasets": [ { "name": "body_condition_measurement_estimates", "title": "Sample MCMC output", "object": "body_condition_measurement_estimates", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "body_condition_measurements", "title": "Humpback whale measurement data from Duke University's Marine Robotics and Remote Sensing (MaRRS) Lab", "object": "body_condition_measurements", "class": [ "data.frame" ], "fields": [ "Animal_ID", "TL", "TL.10.0..Width", "TL.15.0..Width", "TL.20.0..Width", "TL.25.0..Width", "TL.30.0..Width", "TL.35.0..Width", "TL.40.0..Width", "TL.45.0..Width", "TL.5.0..Width", "TL.50.0..Width", "TL.55.0..Width", "TL.60.0..Width", "TL.65.0..Width", "TL.70.0..Width", "TL.75.0..Width", "TL.80.0..Width", "TL.85.0..Width", "TL.90.0..Width", "TL.95.0..Width", "Image", "BaroAlt", "LaserAlt", "Focal_Length", "Iw", "Sw", "Aircraft" ], "rows": 29, "table": true, "tojson": true }, { "name": "calibration", "title": "Calibration (training) data", "object": "calibration", "class": [ "data.frame" ], "fields": [ "CO.ID", "Lpix", "CO.L", "image", "Baro_Alt", "Laser_Alt", "Focal_Length", "Iw", "Sw", "uas" ], "rows": 657, "table": true, "tojson": true }, { "name": "calibration2", "title": "Calibration (training) data from Duke University's Marine Robotics and Remote Sensing (MaRRS) Lab", "object": "calibration2", "class": [ "data.frame" ], "fields": [ "L_train", "RRR.pix", "Images", "Baro...Ht", "Laser_Alt", "Focal.length", "Iw", "Sw", "Aircraft" ], "rows": 46, "table": true, "tojson": true }, { "name": "co_data", "title": "Calibration (training) data for gray whale example", "object": "co_data", "class": [ "data.frame" ], "fields": [ "uas", "CO.ID", "CO.L", "year", "image", "date", "Sw", "Iw", "Focal_Length", "Focal_Length_adj", "Baro_raw", "Launch_Ht", "Baro_Alt", "Laser_Alt", "Lpix" ], "rows": 118, "table": true, "tojson": true }, { "name": "gw_data", "title": "Gray whale measurement data", "object": "gw_data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "whale_ID", "image", "year", "DOY", "uas", "Focal_Length", "Focal_Length_adj", "Sw", "Iw", "Baro_raw", "Launch_Ht", "Baro_Alt", "Laser_Alt", "CO.ID", "TL_px", "TL_w05.00_px", "TL_w10.00_px", "TL_w15.00_px", "TL_w20.00_px", "TL_w25.00_px", "TL_w30.00_px", "TL_w35.00_px", "TL_w40.00_px", "TL_w45.00_px", "TL_w50.00_px", "TL_w55.00_px", "TL_w60.00_px", "TL_w65.00_px", "TL_w70.00_px", "TL_w75.00_px", "TL_w80.00_px", "TL_w85.00_px", "TL_w90.00_px", "TL_w95.00_px" ], "rows": 15, "table": true, "tojson": true }, { "name": "whale_info", "title": "Gray whale metadata", "object": "whale_info", "class": [ "data.frame" ], "fields": [ "Year", "Subject", "Group", "ObservedAge", "AgeType" ], "rows": 293, "table": true, "tojson": true }, { "name": "whales", "title": "Gray whale metadata", "object": "whales", "class": [ "data.frame" ], "fields": [ "whale_ID", "sex", "Age", "AgeType", "year", "date", "Image", "AltitudeBarometer", "AltitudeLaser", "FocalLength", "ImageWidth", "SensorWidth", "UAS", "TL.pix" ], "rows": 826, "table": true, "tojson": true } ], "_help": [ { "page": "body_condition", "title": "Compute body condition metrics for a set of measurements", "topics": [ "body_condition" ] }, { "page": "body_condition_measurement_estimates", "title": "Sample MCMC output", "topics": [ "body_condition_measurement_estimates" ] }, { "page": "body_condition_measurements", "title": "Humpback whale measurement data from Duke University's Marine Robotics and Remote Sensing (MaRRS) Lab", "topics": [ "body_condition_measurements" ] }, { "page": "breakFun", "title": "Break function (required in models)", "topics": [ "breakFun" ] }, { "page": "calibration", "title": "Calibration (training) data", "topics": [ "calibration" ] }, { "page": "calibration_sampler", "title": "MCMC sampler for calibration data", "topics": [ "calibration_sampler" ] }, { "page": "calibration2", "title": "Calibration (training) data from Duke University's Marine Robotics and Remote Sensing (MaRRS) Lab", "topics": [ "calibration2" ] }, { "page": "co_data", "title": "Calibration (training) data for gray whale example", "topics": [ "co_data" ] }, { "page": "combine_observations", "title": "Combine parsed observations into a single parsed object", "topics": [ "combine_observations" ] }, { "page": "flatten_data", "title": "Reformat photogrammetric data for model-based analysis", "topics": [ "flatten_data" ] }, { "page": "growth_curve_sampler", "title": "MCMC sampler for measurements of individuals with replicates and age information to generate growth curve", "topics": [ "growth_curve_sampler" ] }, { "page": "gw_data", "title": "Gray whale measurement data", "topics": [ "gw_data" ] }, { "page": "independent_length_sampler", "title": "MCMC sampler for individuals with independent measurements.", "topics": [ "independent_length_sampler" ] }, { "page": "nondecreasing_length_sampler", "title": "MCMC sampler for measurements of individuals with replicates but no age information.", "topics": [ "nondecreasing_length_sampler" ] }, { "page": "parse_observations", "title": "Pre-process training and experimental data from wide-format to long-format", "topics": [ "parse_observations" ] }, { "page": "whale_info", "title": "Gray whale metadata", "topics": [ "whale_info" ] }, { "page": "whales", "title": "Gray whale metadata", "topics": [ "whales" ] } ], "_readme": "https://github.com/mmi-codex/xcertainty/raw/HEAD/README.md", "_rundeps": [ "cli", "coda", "cpp11", "dplyr", "generics", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "nimble", "numDeriv", "pillar", "pkgconfig", "pracma", "purrr", "R6", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "Xcertainty.Rmd", "filename": "Xcertainty.html", "title": "Xcertainty", "author": "KC Bierlich & Josh Hewitt, CODEX", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Main inputs", "Example: Gray whale body length and body condition", "Calibration Objects", "Gray whale measurements", "Build sampler", "Run Sampler", "View Sampler Outputs (TL and widths)", "Body Condition" ], "created": "2024-03-29 21:26:18", "modified": "2024-10-25 22:57:10", "commits": 16 }, { "source": "Xcertainty_growth_curves.Rmd", "filename": "Xcertainty_growth_curves.html", "title": "Xcertainty Growth Curves", "author": "KC Bierlich & Josh Hewitt, CODEX", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data", "Calibration data", "parse_observations()", "The sampler", "View Sampler Outputs", "Plot Growth Curves" ], "created": "2024-08-24 01:13:41", "modified": "2024-10-25 22:57:10", "commits": 13 }, { "source": "Xcertainty_informative_priors.Rmd", "filename": "Xcertainty_informative_priors.html", "title": "Xcertainty informative priors", "author": "KC Bierlich & Josh Hewitt, CODEX", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example: Gray whale body length", "Calibration Objects", "Gray whale measurements", "Build sampler (non-informative priors)", "Run Sampler", "View Sampler Outputs (TL and widths)", "Trouble Shooting", "Informative priors" ], "created": "2024-08-31 00:49:22", "modified": "2024-10-25 22:57:10", "commits": 6 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": "xcertainty", "_universes": [ "mmi-codex" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-05-24T09:32:47.000Z", "distro": "noble", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "289fb937273d66d2f650facdc73f57478f27b9105acd9007b60adc7abd41f8a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-05-24T09:32:45.000Z", "distro": "noble", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "e102ba4d73d0cc8d36670c030959d49340beb8c1a6d37e5759fc7e70a825139a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-05-24T09:32:11.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "174874f49f734bbc03be413edcadb7655cb39c689afec3ee7c9dcd6ef6db6490", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-05-24T09:32:06.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "a8cbf7c91e6e2bb5aefc788a45ea861038052647c71cf66f944aad05b61915ea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-05-24T09:32:32.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "51c6d3f8d094939435967a5363a43c7973d20fc89fb6889e97d1aed148bae7df", "status": "success", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-05-24T09:31:59.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "8463b33705c35e318c3318fcd2f59998b3d6d5eb65fb11169243ce7abf446b11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-05-24T09:31:52.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "ab2767b0be976bd8343548a273a64d1dff32898cce138a3dfbeb00c1ee811faa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-05-24T09:31:34.000Z", "commit": "8bddc787820681a6c01857667510922285328567", "fileid": "fcf2e4e026e9d66af84f657d5bbadee6e4c580aef0790543bfe8649864adb452", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mmi-codex/actions/runs/26357550083" } ] }