{
  "_id": "6a10004aacfb0bcc41c7af92",
  "Package": "OpenSpecy",
  "Type": "Package",
  "Title": "Analyze, Process, Identify, and Share Raman and (FT)IR Spectra",
  "Version": "1.7.1",
  "Date": "2025-09-29",
  "Authors@R": "c(person(\"Win\", \"Cowger\", role = c(\"cre\", \"aut\", \"dtc\"),\nemail = \"wincowger@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9226-3104\")),\nperson(\"Zacharias\", \"Steinmetz\", role = c(\"aut\"),\nemail = \"z.steinmetz@rptu.de\",\ncomment = c(ORCID = \"0000-0001-6675-5033\")),\nperson(\"Hazel\", \"Vaquero\", role = c(\"aut\"),\nemail = \"hvaquero98@gmail.com\",\ncomment = c(ORCID = \"0009-0001-5468-2049\")),\nperson(\"Nick\", \"Leong\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0008-3313-4132\")),\nperson(\"Andrea\", \"Faltynkova\", role = c(\"aut\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-2523-3137\")),\nperson(\"Hannah\", \"Sherrod\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0001-0497-8693\")),\nperson(\"Andrew B\", \"Gray\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-2252-7367\")),\nperson(\"Hannah\", \"Hapich\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-0000-6632\")),\nperson(\"Jennifer\", \"Lynch\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-3572-8782\")),\nperson(\"Hannah\", \"De Frond\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-1199-0727\")),\nperson(\"Garth\", \"Covernton\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-3814-4918\")),\nperson(\"Keenan\", \"Munno\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-2916-5944\")),\nperson(\"Chelsea\", \"Rochman\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0002-7624-711X\")),\nperson(\"Sebastian\", \"Primpke\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0001-7633-8524\")),\nperson(\"Orestis\", \"Herodotou\", role = c(\"ctb\")),\nperson(\"Mary C\", \"Norris\", role = c(\"ctb\")),\nperson(\"Christine M\", \"Knauss\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-4404-8922\")),\nperson(\"Aleksandra\", \"Karapetrova\", role = c(\"ctb\", \"dtc\", \"rev\"),\ncomment = c(ORCID = \"0000-0002-9856-1644\")),\nperson(\"Vesna\", \"Teofilovic\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-3557-1482\")),\nperson(\"Laura A. T.\", \"Markley\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-0620-8366\")),\nperson(\"Shreyas\", \"Patankar\", role = c(\"ctb\", \"dtc\")),\nperson(\"Rachel\", \"Kozloski\", role = c(\"ctb\", \"dtc\"),\ncomment = c(ORCID = \"0000-0003-1211-9351\")),\nperson(\"Samiksha\", \"Singh\", role = c(\"ctb\")),\nperson(\"Katherine\", \"Lasdin\", role = c(\"ctb\")),\nperson(\"Cristiane\", \"Vidal\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-6363-9475\")),\nperson(\"Clare\", \"Murphy-Hagan\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0009-9629-2856\")),\nperson(\"Philipp\", \"Baumann\", role = c(\"ctb\"),\nemail = \"info@spectral-cockpit.space\",\ncomment = c(ORCID = \"0000-0002-3194-8975\")),\nperson(\"Pierre\", \"Roudier\", role = c(\"ctb\")),\nperson(\"National Renewable Energy Laboratory\", role = c(\"fnd\")),\nperson(\"Possibility Lab\", role = c(\"fnd\")))",
  "Description": "Raman and (FT)IR spectral analysis tool for plastic\nparticles and other environmental samples (Cowger et al. 2025,\n<doi:10.1021/acs.analchem.5c00962>). With read_any(), Open\nSpecy provides a single function for reading individual, batch,\nor map spectral data files like .asp, .csv, .jdx, .spc, .spa,\n.0, and .zip. process_spec() simplifies processing spectra,\nincluding smoothing, baseline correction, range restriction and\nflattening, intensity conversions, wavenumber alignment, and\nmin-max normalization. Spectra can be identified in batch using\nan onboard reference library using match_spec(). A Shiny app is\navailable via run_app() or online at\n<https://www.openanalysis.org/openspecy/>.",
  "URL": "https://github.com/wincowgerDEV/OpenSpecy-package/,\nhttps://raw.githack.com/wincowgerDEV/OpenSpecy-package/main/docs/index.html",
  "BugReports": "https://github.com/wincowgerDEV/OpenSpecy-package/issues/",
  "License": "CC BY 4.0",
  "Encoding": "UTF-8",
  "LazyLoad": "true",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "cmake make libhdf5-dev libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://wincowgerdev.r-universe.dev",
  "Date/Publication": "2026-05-22 03:08:53 UTC",
  "RemoteUrl": "https://github.com/wincowgerdev/openspecy-package",
  "RemoteRef": "HEAD",
  "RemoteSha": "99c27dd9f3c37836a5f5f62050e1bc0772c6ced6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-22 06:59:44 UTC",
    "User": "root"
  },
  "Author": "Win Cowger [cre, aut, dtc] (ORCID:\n<https://orcid.org/0000-0001-9226-3104>),\nZacharias Steinmetz [aut] (ORCID:\n<https://orcid.org/0000-0001-6675-5033>),\nHazel Vaquero [aut] (ORCID: <https://orcid.org/0009-0001-5468-2049>),\nNick Leong [aut] (ORCID: <https://orcid.org/0009-0008-3313-4132>),\nAndrea Faltynkova [aut, dtc] (ORCID:\n<https://orcid.org/0000-0003-2523-3137>),\nHannah Sherrod [aut] (ORCID: <https://orcid.org/0009-0001-0497-8693>),\nAndrew B Gray [ctb] (ORCID: <https://orcid.org/0000-0003-2252-7367>),\nHannah Hapich [ctb] (ORCID: <https://orcid.org/0000-0003-0000-6632>),\nJennifer Lynch [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0003-3572-8782>),\nHannah De Frond [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0003-1199-0727>),\nGarth Covernton [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0003-3814-4918>),\nKeenan Munno [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0003-2916-5944>),\nChelsea Rochman [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0002-7624-711X>),\nSebastian Primpke [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0001-7633-8524>),\nOrestis Herodotou [ctb],\nMary C Norris [ctb],\nChristine M Knauss [ctb] (ORCID:\n<https://orcid.org/0000-0003-4404-8922>),\nAleksandra Karapetrova [ctb, dtc, rev] (ORCID:\n<https://orcid.org/0000-0002-9856-1644>),\nVesna Teofilovic [ctb] (ORCID: <https://orcid.org/0000-0002-3557-1482>),\nLaura A. T. Markley [ctb] (ORCID:\n<https://orcid.org/0000-0003-0620-8366>),\nShreyas Patankar [ctb, dtc],\nRachel Kozloski [ctb, dtc] (ORCID:\n<https://orcid.org/0000-0003-1211-9351>),\nSamiksha Singh [ctb],\nKatherine Lasdin [ctb],\nCristiane Vidal [ctb] (ORCID: <https://orcid.org/0000-0001-6363-9475>),\nClare Murphy-Hagan [ctb] (ORCID:\n<https://orcid.org/0009-0009-9629-2856>),\nPhilipp Baumann [ctb] (ORCID: <https://orcid.org/0000-0002-3194-8975>),\nPierre Roudier [ctb],\nNational Renewable Energy Laboratory [fnd],\nPossibility Lab [fnd]",
  "Maintainer": "Win Cowger <wincowger@gmail.com>",
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    "count": 261,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/OpenSpecy"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OpenSpecy.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/wincowgerdev/openspecy-package",
  "_realowner": "wincowgerdev",
  "_cranurl": true,
  "_releases": [
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      "version": "0.8.2",
      "date": "2021-03-31"
    },
    {
      "version": "0.9.0",
      "date": "2021-04-09"
    },
    {
      "version": "0.9.1",
      "date": "2021-04-11"
    },
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      "version": "0.9.2",
      "date": "2021-05-20"
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      "version": "0.9.3",
      "date": "2021-10-13"
    },
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      "version": "0.9.5",
      "date": "2022-07-06"
    },
    {
      "version": "1.0.2",
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      "date": "2023-09-13"
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      "date": "2024-03-14"
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      "date": "2024-11-04"
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      "date": "2025-04-26"
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  ],
  "_exports": [
    "adj_intens",
    "adj_neg",
    "adj_res",
    "adj_wave",
    "ai_classify",
    "area_under_band",
    "as_hyperSpec",
    "as_OpenSpecy",
    "as_Specs",
    "assess_spec",
    "c_spec",
    "calc_window_points",
    "check_lib",
    "check_OpenSpecy",
    "check_Specs",
    "collapse_spec",
    "conform_res",
    "conform_spec",
    "cor_spec",
    "decompress_spec",
    "def_features",
    "fill_spec",
    "filter_spec",
    "fit_specs_pca",
    "flatten_range",
    "gen_grid",
    "get_lib",
    "get_metadata",
    "heatmap_spec",
    "human_ts",
    "ident_spec",
    "interactive_plot",
    "is_empty_vector",
    "is_OpenSpecy",
    "is_Specs",
    "load_lib",
    "make_rel",
    "manage_na",
    "match_spec",
    "max_cor_named",
    "mean_replace",
    "merge_map",
    "OpenSpecy",
    "os_similarity",
    "plotly_spec",
    "process_spec",
    "read_any",
    "read_asp",
    "read_envi",
    "read_extdata",
    "read_h5",
    "read_jdx",
    "read_many",
    "read_opus",
    "read_opus_raw",
    "read_spa",
    "read_spc",
    "read_spec",
    "read_specs",
    "read_text",
    "read_zip",
    "restrict_range",
    "rm_lib",
    "run_app",
    "sample_spec",
    "sig_noise",
    "smooth_intens",
    "spatial_smooth",
    "spec_res",
    "Specs",
    "split_spec",
    "subtr_baseline",
    "write_spec",
    "write_specs"
  ],
  "_datasets": [
    {
      "name": "raman_hdpe",
      "title": "Sample Raman spectrum",
      "object": "raman_hdpe",
      "class": [
        "OpenSpecy",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "test_lib",
      "title": "Test reference library",
      "object": "test_lib",
      "class": [
        "OpenSpecy",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adj_intens",
      "title": "Adjust spectral intensities to standard absorbance units.",
      "topics": [
        "adj_intens",
        "adj_intens.default",
        "adj_intens.OpenSpecy"
      ]
    },
    {
      "page": "data_norm",
      "title": "Normalization and conversion of spectral data",
      "topics": [
        "adj_neg",
        "adj_res",
        "conform_res",
        "is_empty_vector",
        "mean_replace"
      ]
    },
    {
      "page": "adj_wave",
      "title": "Adjust wavelength to wavenumbers for Raman",
      "topics": [
        "adj_wave",
        "adj_wave.default",
        "adj_wave.OpenSpecy"
      ]
    },
    {
      "page": "area_under_band",
      "title": "Measure the area under band of spectra",
      "topics": [
        "area_under_band",
        "area_under_band.default",
        "area_under_band.OpenSpecy"
      ]
    },
    {
      "page": "as_OpenSpecy",
      "title": "Create 'OpenSpecy' objects",
      "topics": [
        "as_OpenSpecy",
        "as_OpenSpecy.data.frame",
        "as_OpenSpecy.default",
        "as_OpenSpecy.hyperSpec",
        "as_OpenSpecy.list",
        "as_OpenSpecy.OpenSpecy",
        "check_OpenSpecy",
        "gen_grid",
        "is_OpenSpecy",
        "OpenSpecy"
      ]
    },
    {
      "page": "assess_spec",
      "title": "Assess common spectral quality issues",
      "topics": [
        "assess_spec",
        "assess_spec.default",
        "assess_spec.OpenSpecy"
      ]
    },
    {
      "page": "manage_spec",
      "title": "Manage spectral objects",
      "topics": [
        "c_spec",
        "c_spec.default",
        "c_spec.list",
        "c_spec.OpenSpecy",
        "merge_map",
        "merge_map.default",
        "merge_map.list",
        "merge_map.OpenSpecy",
        "sample_spec",
        "sample_spec.default",
        "sample_spec.OpenSpecy"
      ]
    },
    {
      "page": "manage_lib",
      "title": "Manage spectral libraries",
      "topics": [
        "check_lib",
        "get_lib",
        "load_lib",
        "rm_lib"
      ]
    },
    {
      "page": "def_features",
      "title": "Define features",
      "topics": [
        "collapse_spec",
        "collapse_spec.default",
        "collapse_spec.OpenSpecy",
        "def_features",
        "def_features.default",
        "def_features.OpenSpecy"
      ]
    },
    {
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    {
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    {
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    {
      "page": "read_ext",
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      "source": "sop.Rmd",
      "filename": "sop.html",
      "title": "Open Specy Package Tutorial",
      "author": "Win Cowger, Zacharias Steinmetz, Rachel Kozloski, Aleksandra Karapetrova",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Document Overview",
        "Installation",
        "Running the App",
        "Read Data",
        "Save Data",
        "Format Conversions",
        "Visualization",
        "Spectra",
        "Maps",
        "Combining OpenSpecy Objects",
        "Filtering OpenSpecy Objects",
        "Sampling OpenSpecy Objects",
        "Processing",
        "Threshold Signal and Noise",
        "Intensity Adjustment",
        "Conforming",
        "Smoothing",
        "Baseline Correction",
        "Flattening Ranges",
        "Identifying Spectra",
        "Reading Libraries",
        "Matches",
        "Library Metadata",
        "Plot Matches",
        "Sharing Reference Data",
        "Characterizing Particles",
        "Brute Force",
        "A Priori Particle Thresholding",
        "References"
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      "created": "2021-03-22 10:48:55",
      "modified": "2025-04-26 17:45:16",
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