{ "_id": "6a1f0c72b401979e7341cb2d", "Package": "tagtools", "Title": "Work with Data from High-Resolution Biologging Tags", "Version": "0.3.0", "Authors@R": "c(person(\"Stacy\", \"DeRuiter\", \nemail = \"stacy.deruiter@calvin.edu\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-0571-0306\")),\nperson(\"Mark\", \"Johnson\",\nrole = c(\"aut\", \"cph\")),\nperson(\"David\", \"Sweeney\",\nrole = \"aut\"),\nperson(\"Ye Joo\", \"McNamara-Oh\",\nrole = \"aut\"),\nperson(\"Samuel\", \"Fynewever\",\nrole = \"aut\"),\nperson(\"(Oghenkevwe) Racheal\", \"Tejevbo\",\nrole = \"aut\"),\nperson(\"Tiago\", \"Marques\",\nrole = \"aut\"),\nperson(\"Yuqian\", \"Wang\",\nrole = c(\"aut\")),\nperson(\"(Oghenesuvwe) Su\", \"Ogedegbe\",\nrole = \"aut\"))", "Description": "High-resolution movement-sensor tags typically include\naccelerometers to measure body posture and sudden movements or\nchanges in speed, magnetometers to measure direction of travel,\nand pressure sensors to measure dive depth in aquatic or marine\nanimals. The sensors in these tags usually sample many times\nper second. Some tags include sensors for speed, turning rate\n(gyroscopes), and sound. This package provides software tools\nto facilitate calibration, processing, and analysis of such\ndata. Tools are provided for: data import/export; calibration\n(from raw data to calibrated data in scientific units);\nvisualization (for example, multi-panel time-series plots);\ndata processing (such as event detection, calculation of\nderived metrics like jerk and dynamic acceleration, dive\ndetection, and dive parameter calculation); and statistical\nanalysis (for example, track reconstruction, a rotation test,\nand Mahalanobis distance analysis).", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "URL": "https://animaltags.org,\nhttps://animaltags.github.io/tagtools_r/index.html", "BugReports": "https://github.com/animaltags/tagtools_r/issues", "Config/Needs/website": "rmarkdown", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libnetcdf-dev\nlibssl-dev libx11-dev", "Repository": "https://animaltags.r-universe.dev", "Date/Publication": "2026-04-17 20:37:33 UTC", "RemoteUrl": "https://github.com/animaltags/tagtools_r", "RemoteRef": "HEAD", "RemoteSha": "a113152fc3907025546d2dac8f9b490996a9a5c7", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-17 09:31:02 UTC", "User": "root" }, "Author": "Stacy DeRuiter [aut, cre, cph] (ORCID:\n),\nMark Johnson [aut, cph],\nDavid Sweeney [aut],\nYe Joo McNamara-Oh [aut],\nSamuel Fynewever [aut],\n(Oghenkevwe) Racheal Tejevbo [aut],\nTiago Marques [aut],\nYuqian Wang [aut],\n(Oghenesuvwe) Su Ogedegbe [aut]", "Maintainer": "Stacy DeRuiter ", "MD5sum": "622d8e66166103abeb7ef915f4a8e2de", "_user": "animaltags", "_type": "src", "_file": "tagtools_0.3.0.tar.gz", "_fileid": "42d26743a4b9fd12707742f9435718ec0618e06a76a9206daeec360498470197", "_filesize": 1309572, "_sha256": "42d26743a4b9fd12707742f9435718ec0618e06a76a9206daeec360498470197", "_created": "2026-05-17T09:31:02.000Z", "_published": "2026-06-02T17:01:38.056Z", "_distro": "noble", "_jobs": [ { "job": 79126760611, "time": 170, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7041259329" }, { "job": 79126760367, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7041259573" }, { "job": 79126760701, "time": 203, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7041263150" }, { "job": 79126760212, "time": 164, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7041258727" }, { "job": 79126760718, "time": 211, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7041260190" }, { "job": 79126761321, "time": 370, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7041276889" }, { "job": 79126760441, "time": 164, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7041256093" }, { "job": 79126760643, "time": 261, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7041267599" }, { "job": 79126759835, "time": 217, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7041238969" }, { "job": 79126759629, "time": 136, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7364493737" }, { "job": 79126760340, "time": 157, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7041257984" }, { "job": 79126760903, "time": 134, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7041255158" }, { "job": 79126761003, "time": 147, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7041256667" } ], "_buildurl": "https://github.com/r-universe/animaltags/actions/runs/25987091332", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/animaltags/tagtools_r", "_commit": { "id": "a113152fc3907025546d2dac8f9b490996a9a5c7", "author": "stacyderuiter ", "committer": "stacyderuiter ", "message": "fix typo added to zero_crossings() in last commit\n", "time": 1776458253 }, "_maintainer": { "name": "Stacy DeRuiter", "email": "stacy.deruiter@calvin.edu", "login": "stacyderuiter", "twitter": "@slderuiter", "description": "", "uuid": 5868268, "orcid": "0000-0002-0571-0306" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "CircStats", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "gsignal", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "ncdf4", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "zoom", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "animaltags", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 4 }, { "week": "2025-45", "n": 2 }, { "week": "2025-47", "n": 3 }, { "week": "2025-48", "n": 3 }, { "week": "2025-49", "n": 4 }, { "week": "2025-50", "n": 6 }, { "week": "2025-51", "n": 2 }, { "week": "2026-02", "n": 4 }, { "week": "2026-05", "n": 1 }, { "week": "2026-07", "n": 1 }, { "week": "2026-16", "n": 3 } ], "_tags": [], "_stars": 8, "_contributors": [ { "user": "stacyderuiter", "count": 92, "uuid": 5868268 }, { "user": "ewikun", "count": 57, "uuid": 122011603 }, { "user": "osuvwe1", "count": 43, "uuid": 64463922 } ], "_userbio": { "uuid": 95633841, "type": "organization", "name": "animaltags" }, "_downloads": { "count": 218, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tagtools" }, "_devurl": "https://github.com/animaltags/tagtools_r", "_searchresults": 41, "_topics": [ "openblas", "cpp", "openmp" ], "_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/tagtools.html", "manual.pdf" ], "_homeurl": "https://github.com/animaltags/tagtools_r", "_realowner": "animaltags", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2023-07-18" }, { "version": "0.2.0", "date": "2024-06-28" }, { "version": "0.3.0", "date": "2025-12-18" } ], "_exports": [ "a2pr", "absorption", "acc_wgs84", "add_nc", "apply_cal", "block_acf", "block_mean", "block_rms", "body_axes", "buffer", "check_AM", "cline", "col_line3", "comp_filt", "conv_cpp", "crop", "crop_all", "crop_to", "csv2struct", "decdc", "decz", "depth_rate", "depth2pressure", "detect_peaks", "dive_stats", "draw_axis", "dsf", "euler2rotmat", "extract", "extract_cues", "find_dives", "fir_nodelay", "fit_tracks", "fix_offset_3d", "fix_pressure", "get_br", "hilbert_env", "hilbert_transform", "htrack", "image_irreg", "inclination", "interp_nan", "interp2length", "inv_axis", "julian_day", "lalo2llf", "load_nc", "m_dist", "m2h", "make_info", "make_specgram", "mean_absorption", "median_filter", "merge_fields", "metadata_editor", "msa", "njerk", "norm2", "ocdr", "odba", "plott", "plott_base", "prh_predictor1", "prh_predictor2", "ptrack", "read_cats", "read_cats_csv", "rotate_data", "rotate_vecs", "rotation_test", "rotmat2euler", "rough_cal_3d", "save_nc", "sens_struct", "smooth", "sound_speed", "spectrum_level", "speed_from_depth", "spherical_cal", "tag2animal", "tortuosity", "track3D", "undo_cal", "zero_crossings" ], "_datasets": [ { "name": "beaked_whale", "title": "Set of sensor lists for a beaked_whale", "object": "beaked_whale", "class": [ "animaltag", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "harbor_seal", "title": "Set of sensor lists for a harbor seal", "object": "harbor_seal", "class": [ "animaltag", "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "a2pr", "title": "Pitch and roll from acceleration", "topics": [ "a2pr" ] }, { "page": "absorption", "title": "Calculates the absorption coefficient for sound in seawater", "topics": [ "absorption" ] }, { "page": "acc_wgs84", "title": "Calculate total acceleration", "topics": [ "acc_wgs84" ] }, { "page": "add_nc", "title": "Save an item to a NetCDF or add one tag sensor or metadata variable to a NetCDF archive file.", "topics": [ "add_nc" ] }, { "page": "apply_cal", "title": "Implement a calibration on tag sensor data", "topics": [ "apply_cal" ] }, { "page": "beaked_whale", "title": "Set of sensor lists for a beaked_whale", "topics": [ "beaked_whale" ] }, { "page": "block_acf", "title": "Compute autocorrelation function", "topics": [ "block_acf" ] }, { "page": "block_mean", "title": "Compute mean of sample blocks", "topics": [ "block_mean" ] }, { "page": "block_rms", "title": "Compute RMS of sample blocks", "topics": [ "block_rms" ] }, { "page": "body_axes", "title": "Generate the cardinal axes of an animal", "topics": [ "body_axes" ] }, { "page": "buffer", "title": "Buffers a signal vector into matrix", "topics": [ "buffer" ] }, { "page": "check_AM", "title": "Compute field intensity of tag acceleration and magnetometer data.", "topics": [ "check_AM" ] }, { "page": "cline", "title": "Add colored line segments to a plot", "topics": [ "cline" ] }, { "page": "col_line3", "title": "Plot coloured line(s) in 3 dimensions with plot_ly", "topics": [ "col_line3" ] }, { "page": "comp_filt", "title": "Complementary filtering of a signal.", "topics": [ "comp_filt" ] }, { "page": "conv_cpp", "title": "Convolution (in C++)", "topics": [ "conv_cpp" ] }, { "page": "crop", "title": "Interactive data cropping tool.", "topics": [ "crop" ] }, { "page": "crop_all", "title": "Reduce the time span of a dataset", "topics": [ "crop_all" ] }, { "page": "crop_to", "title": "Reduce the time span of data", "topics": [ "crop_to" ] }, { "page": "csv2struct", "title": "Read tag metadata from csv", "topics": [ "csv2struct" ] }, { "page": "decdc", "title": "Reduce the sampling rate", "topics": [ "decdc" ] }, { "page": "decz", "title": "Decimate sampling rate recursively.", "topics": [ "decz" ] }, { "page": "depth_rate", "title": "Estimate the vertical velocity", "topics": [ "depth_rate" ] }, { "page": "depth2pressure", "title": "Convert depth to pressure", "topics": [ "depth2pressure" ] }, { "page": "detect_peaks", "title": "Detect peaks in signal vector data", "topics": [ "detect_peaks" ] }, { "page": "dive_stats", "title": "Compute summary statistics for dives or flights", "topics": [ "dive_stats" ] }, { "page": "draw_axis", "title": "Draw time axis on plott plot.", "topics": [ "draw_axis" ] }, { "page": "dsf", "title": "Estimate the dominant stroke frequency", "topics": [ "dsf" ] }, { "page": "euler2rotmat", "title": "Make a rotation (or direction cosine) matrix", "topics": [ "euler2rotmat" ] }, { "page": "extract", "title": "Extract a sub-sample of data", "topics": [ "extract" ] }, { "page": "extract_cues", "title": "Extract multiple sub-samples of data", "topics": [ "extract_cues" ] }, { "page": "find_dives", "title": "Find time cues for dives", "topics": [ "find_dives" ] }, { "page": "fir_nodelay", "title": "Delay-free filtering", "topics": [ "fir_nodelay" ] }, { "page": "fit_tracks", "title": "Integrate track with reference positions", "topics": [ "fit_tracks" ] }, { "page": "fix_offset_3d", "title": "Estimate the offset in each axis", "topics": [ "fix_offset_3d" ] }, { "page": "fix_pressure", "title": "Correct a depth or altitude profile", "topics": [ "fix_pressure" ] }, { "page": "get_br", "title": "Use magnetometer data to estimate the body rotations from cyclic locomotion movements.", "topics": [ "get_br" ] }, { "page": "get_researcher", "title": "Find matching researcher in a list of known tag researchers", "topics": [ "get_researcher" ] }, { "page": "get_species", "title": "Find matching species in a list of marine mammals", "topics": [ "get_species" ] }, { "page": "harbor_seal", "title": "Set of sensor lists for a harbor seal", "topics": [ "harbor_seal" ] }, { "page": "hilbert_env", "title": "Compute the envelope of X using Hilbert transform. Compute the envelope of the signal matrix X using the Hilbert transform. To avoid long transforms, this function uses the overlap and add method.", "topics": [ "hilbert_env" ] }, { "page": "hilbert_transform", "title": "Return the Hilbert transform of a signal", "topics": [ "hilbert_transform" ] }, { "page": "htrack", "title": "Simple horizontal dead-reckoned track", "topics": [ "htrack" ] }, { "page": "image_irreg", "title": "Plot an image with an irregular grid.", "topics": [ "image_irreg" ] }, { "page": "inclination", "title": "Estimate the inclination angle", "topics": [ "inclination" ] }, { "page": "interp_nan", "title": "Remove NAs from sensor data and return indices of (rows of) filled values", "topics": [ "interp_nan" ] }, { "page": "interp2length", "title": "Interpolate regularly sampled data to increase its sampling rate and match its length to another variable.", "topics": [ "interp2length" ] }, { "page": "inv_axis", "title": "Identify invariant axis in triaxial movement measurements.", "topics": [ "inv_axis" ] }, { "page": "julian_day", "title": "Convert between dates and Julian day numbers.", "topics": [ "julian_day" ] }, { "page": "lalo2llf", "title": "Convert latitude-longitude track points into a local level frame", "topics": [ "lalo2llf" ] }, { "page": "load_nc", "title": "Load a tag dataset from a netCDF file.", "topics": [ "load_nc" ] }, { "page": "m_dist", "title": "Calculate Mahalanobis distance", "topics": [ "m_dist" ] }, { "page": "m2h", "title": "Heading from accelerometer and magnetometer data", "topics": [ "m2h" ] }, { "page": "make_info", "title": "Make an info structure with tag metadata", "topics": [ "make_info" ] }, { "page": "make_specgram", "title": "Plot a spectrogram with default settings", "topics": [ "make_specgram" ] }, { "page": "mean_absorption", "title": "Calculate the mean absorption in salt water", "topics": [ "mean_absorption" ] }, { "page": "median_filter", "title": "Computes the nth-order median filter", "topics": [ "median_filter" ] }, { "page": "merge_fields", "title": "Merge the fields of two lists", "topics": [ "merge_fields" ] }, { "page": "metadata_editor", "title": "Edits a html file from given csv.", "topics": [ "metadata_editor" ] }, { "page": "msa", "title": "Compute MSA", "topics": [ "msa" ] }, { "page": "njerk", "title": "Compute the norm-jerk", "topics": [ "njerk" ] }, { "page": "norm2", "title": "Compute the row-wise vector norm", "topics": [ "norm2" ] }, { "page": "ocdr", "title": "Estimate the forward speed", "topics": [ "ocdr" ] }, { "page": "odba", "title": "Compute ODBA", "topics": [ "odba" ] }, { "page": "plott", "title": "Plot tag data time series", "topics": [ "plott" ] }, { "page": "plott_base", "title": "Plot tag data time series", "topics": [ "plott_base" ] }, { "page": "plott_static_panel", "title": "Helper function for plott", "topics": [ "plott_static_panel" ] }, { "page": "prh_predictor1", "title": "Predict the tag position on a diving animal from depth and acceleration data", "topics": [ "prh_predictor1" ] }, { "page": "prh_predictor2", "title": "Predict the tag position on a diving animal from depth and acceleration data", "topics": [ "prh_predictor2" ] }, { "page": "ptrack", "title": "Estimate simple dead-reckoned track", "topics": [ "ptrack" ] }, { "page": "read_cats", "title": "Read CATS csv data file(s) and convert to .nc", "topics": [ "read_cats" ] }, { "page": "read_cats_csv", "title": "Read a CSV file with sensor data from a CATS tag", "topics": [ "read_cats_csv" ] }, { "page": "rotate_data", "title": "Rotate data.", "topics": [ "rotate_data" ] }, { "page": "rotate_vecs", "title": "Rotate triaxial vector measurements", "topics": [ "rotate_vecs" ] }, { "page": "rotation_test", "title": "Carry out a rotation randomization test.", "topics": [ "rotation_test" ] }, { "page": "rotmat2euler", "title": "Decompose a rotation (or direction cosine) matrix", "topics": [ "rotmat2euler" ] }, { "page": "rough_cal_3d", "title": "Estimate scale factors and offsets", "topics": [ "rough_cal_3d" ] }, { "page": "save_nc", "title": "Save a tag dataset to a netCDF file.", "topics": [ "save_nc" ] }, { "page": "sens_struct", "title": "Generate a sensor structure from a sensor data vector or matrix.", "topics": [ "sens_struct" ] }, { "page": "smooth", "title": "Low pass filter a time series", "topics": [ "smooth" ] }, { "page": "sound_speed", "title": "Sound speed estimation", "topics": [ "sound_speed" ] }, { "page": "spectrum_level", "title": "Compute the spectrum level of a signal x.", "topics": [ "spectrum_level" ] }, { "page": "speed_from_depth", "title": "Estimate the forward speed of a diving animal", "topics": [ "speed_from_depth" ] }, { "page": "spherical_cal", "title": "Deduce the calibration constants", "topics": [ "spherical_cal" ] }, { "page": "tag2animal", "title": "Tag-frame to animal-frame conversion", "topics": [ "tag2animal" ] }, { "page": "tortuosity", "title": "Compute tortuosity index", "topics": [ "tortuosity" ] }, { "page": "track3D", "title": "Reconstruct a track from pitch, heading and depth data, given a starting position", "topics": [ "track3D" ] }, { "page": "undo_cal", "title": "Undo calibrations steps", "topics": [ "undo_cal" ] }, { "page": "zero_crossings", "title": "Find zero-crossings in a vector", "topics": [ "zero_crossings" ] } ], "_readme": "https://github.com/animaltags/tagtools_r/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bit", "bit64", "boot", "bslib", "cachem", "CircStats", "cli", "clipr", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gsignal", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "lubridate", "magrittr", "MASS", "memoise", "mime", "ncdf4", "openssl", "otel", "pillar", "pkgconfig", "plotly", "pracma", "prettyunits", "progress", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", 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