{ "_id": "6a1e880a1d7bb097a0a67da7", "Package": "yaps", "Title": "Track Estimation using YAPS (Yet Another Positioning Solver)", "Version": "1.2.5", "Authors@R": "c(\tperson(\"Henrik\", \"Baktoft\", email = \"hba@aqua.dtu.dk\", role = c(\"cre\", \"aut\"), comment=c(ORCID = \"0000-0002-3644-4960\")),\nperson(\"Karl\", \"Gjelland\", role=c(\"aut\"), comment=c(ORCID = \"0000-0003-4036-4207\")),\nperson(\"Uffe H.\", \"Thygesen\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-4311-6324\")),\nperson(\"Finn\", \"Økland\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-1938-5460\"))\n)", "Description": "Estimate tracks of animals tagged with acoustic\ntransmitters. 'yaps' was introduced in 2017 as a transparent\nopen-source tool to estimate positions of fish (and other\naquatic animals) tagged with acoustic transmitters. Based on\nregistrations of acoustic transmitters on hydrophones\npositioned in a fixed array, 'yaps' enables users to\nsynchronize the collected data (i.e. correcting for drift in\nthe internal clocks of the hydrophones/receivers) and\nsubsequently to estimate tracks of the tagged animals. The\npaper introducing 'yaps' is available in open access at\nBaktoft, Gjelland, Økland & Thygesen (2017)\n. Also check out our cookbook\nwith a completely worked through example at Baktoft, Gjelland,\nØkland, Rehage, Rodemann, Corujo, Viadero & Thygesen (2019)\n. Additional tutorials will\neventually make their way onto the project website at\n.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "Remotes": [ "spkaluzny/splusTimeSeries", "spkaluzny/splusTimeDate" ], "URL": "https://github.com/baktoft/yaps, https://baktoft.github.io/yaps/", "BugReports": "https://github.com/baktoft/yaps/issues", "Config/pak/sysreqs": "cmake libicu-dev", "Repository": "https://benjaminhlina.r-universe.dev", "Date/Publication": "2023-10-26 18:55:56 UTC", "RemoteUrl": "https://github.com/ocean-tracking-network/yaps", "RemoteRef": "HEAD", "RemoteSha": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 07:28:54 UTC", "User": "root" }, "Author": "Henrik Baktoft [cre, aut] (ORCID:\n),\nKarl Gjelland [aut] (ORCID: ),\nUffe H. Thygesen [aut] (ORCID: ),\nFinn Økland [aut] (ORCID: )", "Maintainer": "Henrik Baktoft ", "MD5sum": "84c8ee48feae9e11df4a3d2fd750c393", "_user": "benjaminhlina", "_type": "src", "_file": "yaps_1.2.5.tar.gz", "_fileid": "777ce1225ee875f8cc9da9d0e73161b2c2bf6d276ce58441da1764b59f38a7fa", "_filesize": 2656876, "_sha256": "777ce1225ee875f8cc9da9d0e73161b2c2bf6d276ce58441da1764b59f38a7fa", "_created": "2026-06-02T07:28:54.000Z", "_published": "2026-06-02T07:36:42.889Z", "_distro": "noble", "_jobs": [ { "job": 79020920069, "time": 238, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7351601700" }, { "job": 79020920111, "time": 218, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7351594644" }, { "job": 79020920094, "time": 215, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7351594749" }, { "job": 79020920100, "time": 217, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7351594189" }, { "job": 79020920089, "time": 230, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7351597707" }, { "job": 79020920071, "time": 286, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7351615234" }, { "job": 79020920104, "time": 159, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7351576534" }, { "job": 79020920080, "time": 392, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7351647235" }, { "job": 79020216465, "time": 280, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7351526518" }, { "job": 79020920057, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7351571054" }, { "job": 79020920103, "time": 224, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7351597138" }, { "job": 79020920072, "time": 198, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7351588086" }, { "job": 79020920059, "time": 211, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7351592721" } ], "_buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ocean-tracking-network/yaps", "_commit": { "id": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "author": "Jon Pye ", "committer": "GitHub ", "message": "Update DESCRIPTION\n\nuse github versions of splustimeseries, splustimedate", "time": 1698346556 }, "_maintainer": { "name": "Henrik Baktoft", "email": "hba@aqua.dtu.dk", "login": "baktoft", "description": "", "uuid": 22369824, "orcid": "0000-0002-3644-4960" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "TMB", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "circular", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "nloptr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tictoc", "role": "Imports" }, { "package": "TMB", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "caTools", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "ocean-tracking-network", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "baktoft", "count": 100, "uuid": 22369824 }, { "user": "jennavergeynst", "count": 3, "uuid": 18457551 }, { "user": "jdpye", "count": 1, "uuid": 3063276 } ], "_userbio": { "uuid": 29612410, "type": "user", "name": "Benjamin Hlina", "description": "Postdoctoral Researcher @ GLIER - University of Windsor - Studying food webs and spatial ecology of fishes in Lakes Ontario and Huron." }, "_downloads": { "count": 9, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/yaps" }, "_devurl": "https://github.com/baktoft/yaps", "_pkgdown": "https://baktoft.github.io/yaps/", "_searchresults": 65, "_topics": [ "cpp" ], "_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/yaps.html", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "1.2.4", "date": "2021-02-10" }, { "version": "1.2.5", "date": "2021-04-13" } ], "_exports": [ "alignBurstSeq", "applySync", "checkInp", "checkInpSync", "fineTuneSyncModel", "getBbox", "getInp", "getInpSync", "getSyncCoverage", "getSyncModel", "getToaYaps", "plotBbox", "plotSyncModelCheck", "plotSyncModelHydros", "plotSyncModelResids", "plotYaps", "prepDetections", "runTmb", "runYaps", "simHydros", "simTelemetryTrack", "simToa", "simTrueTrack", "tempToSs", "testYaps" ], "_datasets": [ { "name": "dat_align", "title": "Example data for showcasing yaps function alignBurstSeq()", "object": "dat_align", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ssu1", "title": "Test data from Florida Bay", "object": "ssu1", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "alignBurstSeq", "title": "Align synced data with known burst sequence", "topics": [ "alignBurstSeq" ] }, { "page": "applySync", "title": "Apply sync model to toa matrix to obtain synced data", "topics": [ "applySync" ] }, { "page": "checkInp", "title": "Check consistency of 'inp' object obtained from 'getInp()'", "topics": [ "checkInp" ] }, { "page": "checkInpSync", "title": "Check consistency of 'inp_sync' object obtained from 'getInpSync()'", "topics": [ "checkInpSync" ] }, { "page": "dat_align", "title": "Example data for showcasing yaps function alignBurstSeq()", "topics": [ "dat_align" ] }, { "page": "fineTuneSyncModel", "title": "Fine-tune an already fitted sync_model Wrapper function to re-run getSyncModel() using the same data, but excluding outliers. Note dimensions of data might change if eps_threshold results in empty rows in the TOA-matrix.", "topics": [ "fineTuneSyncModel" ] }, { "page": "getBbox", "title": "Get a standard bounding box to impose spatial constraints", "topics": [ "getBbox" ] }, { "page": "getInp", "title": "Get prepared inp-object for use in TMB-call", "topics": [ "getInp" ] }, { "page": "getInpSync", "title": "Get object inp for synchronization", "topics": [ "getInpSync" ] }, { "page": "getSyncCoverage", "title": "Quick overview to check if all hydros have enough data within each offset period.", "topics": [ "getSyncCoverage" ] }, { "page": "getSyncModel", "title": "Get sync model from inp_sync object obtained by 'getInpSync()'", "topics": [ "getSyncModel" ] }, { "page": "getToaYaps", "title": "Build TOA matrix from synced data.table - also do some pre-filtering of severe MP, pruning loose ends etc", "topics": [ "getToaYaps" ] }, { "page": "plotBbox", "title": "Graphical representation of spatial constraints", "topics": [ "plotBbox" ] }, { "page": "plotSyncModelCheck", "title": "Plot to check how well the sync model is working", "topics": [ "plotSyncModelCheck" ] }, { "page": "plotSyncModelHydros", "title": "Plot hydrophone positions. Especially useful if some hydro re-positioned as part of the sync model.", "topics": [ "plotSyncModelHydros" ] }, { "page": "plotSyncModelResids", "title": "Plot residuals of sync_model to enable check of model", "topics": [ "plotSyncModelResids" ] }, { "page": "plotYaps", "title": "Basic plots of yaps output", "topics": [ "plotYaps" ] }, { "page": "prepDetections", "title": "Experimental! Prepare detections data.table from raw data - csv-files exported from vendor software", "topics": [ "prepDetections" ] }, { "page": "runYaps", "title": "Function to run TMB to estimate track", "topics": [ "runTmb", "runYaps" ] }, { "page": "simHydros", "title": "Sim hydrophone array configuration", "topics": [ "simHydros" ] }, { "page": "simTelemetryTrack", "title": "Simulate telemetry track based on known true track obtained using simTrueTrack", "topics": [ "simTelemetryTrack" ] }, { "page": "simToa", "title": "Sim TOA matrix for the supplied telemetryTrack", "topics": [ "simToa" ] }, { "page": "simTrueTrack", "title": "Simulate a known movement track for subsequent estimation using YAPS", "topics": [ "simTrueTrack" ] }, { "page": "ssu1", "title": "Test data from Florida Bay", "topics": [ "ssu1" ] }, { "page": "tempToSs", "title": "Calculate speed of sound from water temperature, salinity and depth Based on H. Medwin (1975) Speed of sound in water: A simple equation for realistic parameters. (https://doi.org/10.1121/1.380790)", "topics": [ "tempToSs" ] }, { "page": "testYaps", "title": "Test YAPS core functionality", "topics": [ "testYaps" ] } ], "_readme": "https://github.com/ocean-tracking-network/yaps/raw/HEAD/README.md", "_rundeps": [ "boot", "circular", "cli", "cowplot", "cpp11", "data.table", "farver", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "mvtnorm", "nloptr", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "tictoc", "TMB", "vctrs", "viridis", "viridisLite", "withr", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 2.8129133566428557, "_indexed": false, "_nocasepkg": "yaps", "_universes": [ "benjaminhlina" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.5", "date": "2026-06-02T07:32:18.000Z", "distro": "noble", "arch": "aarch64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "bf9b8fb2c2f3090a4c09da07e1d5d378559a5af500f96ad5c1e4d6f5a15e75c8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.7.0", "os": "linux", "version": "1.2.5", "date": "2026-06-02T07:31:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "a06856e930b26a5bb25ba194cd666ddf0ffa58215a550a2d463a8438e5e28174", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "linux", "version": "1.2.5", "date": "2026-06-02T07:32:00.000Z", "distro": "noble", "arch": "aarch64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "93bae12c7e43afaf58751f6b596c9982eb667c6b355712b6eaa9bdd38acb5359", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "linux", "version": "1.2.5", "date": "2026-06-02T07:31:48.000Z", "distro": "noble", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "317403c6e8ae7a1fba27d473ccb495a7dc5e0435fbd323cd3d89721f912567cf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.5.3", "os": "mac", "version": "1.2.5", "date": "2026-06-02T07:31:41.000Z", "arch": "aarch64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "c23dfeb061b0e2ffe5f2e4aaf28e36892aa987e297a95a8e21df4a4717bb6106", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.5.3", "os": "mac", "version": "1.2.5", "date": "2026-06-02T07:32:17.000Z", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "140815a49a1f8cc7b1e245ee73ff52853ffdacc2863c55c2c1928d846d9c0289", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "mac", "version": "1.2.5", "date": "2026-06-02T07:31:13.000Z", "arch": "aarch64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "db13b4cc08012bd35775af076a77844e38fac881b4fd0e8fabc066b916442abc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "mac", "version": "1.2.5", "date": "2026-06-02T07:33:29.000Z", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "9b606689a49f4610c624590c0c7937c035f5070ce8aa0b1e0db61b8297897088", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.5", "date": "2026-06-02T07:31:59.000Z", "arch": "emscripten", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "095cc3b6205d1345c8119ca0166726a9e31ca33d7a401d5e0aa1165c7cfbbbd3", "status": "success", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.7.0", "os": "win", "version": "1.2.5", "date": "2026-06-02T07:31:09.000Z", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "2354eaa1a370674e1b37f7e3efad79047220ec27a54bc2d150a633a97d309147", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.5.3", "os": "win", "version": "1.2.5", "date": "2026-06-02T07:30:46.000Z", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "db1dd553896997460bc27ab6a3a905fc5c02db6db65d62fc8297bcdaca98f366", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" }, { "r": "4.6.0", "os": "win", "version": "1.2.5", "date": "2026-06-02T07:30:50.000Z", "arch": "x86_64", "commit": "6a3f3bccbae413e511dee5ddc80e6ae821fb87d5", "fileid": "44f9d15eb33bd3ee3cb520d9a299132d729f7a65340ea8889d07d80bb308c9aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/benjaminhlina/actions/runs/26804987455" } ] }