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  "Title": "Acquire Data from Ocean Optics Spectrometers",
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  "Date": "2026-10-18",
  "Authors@R": "c(\nperson(\"Pedro J.\", \"Aphalo\", email = \"pedro.aphalo@helsinki.fi\", role = c(\"aut\", \"trl\", \"cre\")),\nperson(\"Lasse\", \"Ylianttila\", role = c(\"aut\")),\nperson(\"Titta K.\", \"Kotilainen\", role = \"ctb\")\n)",
  "Description": "Functions to acquire data directly from Ocean Optics\nspectrometers, and functions to read similar data from files.\nFunctions to convert raw-counts into counts-per-second and\nphysical quantities. Data are saved in objects of classes\ndefined in package 'photobiology'. The instrument settings,\ninstrument description, date-time of acquisition and optionally\ngoecode are stored as attributes.",
  "License": "GPL (>= 2)",
  "Additional_repositories": "https://aphalo.r-universe.dev/",
  "LazyLoad": "yes",
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  "ByteCompile": "true",
  "URL": "https://docs.r4photobiology.info/ooacquire/,\nhttps://github.com/aphalo/ooacquire",
  "BugReports": "https://github.com/aphalo/ooacquire/issues",
  "Encoding": "UTF-8",
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  "Repository": "https://aphalo.r-universe.dev",
  "Date/Publication": "2026-10-17 22:38:04 UTC",
  "RemoteUrl": "https://github.com/aphalo/ooacquire",
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  "Packaged": {
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    "User": "root"
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  "Author": "Pedro J. Aphalo [aut, trl, cre],\nLasse Ylianttila [aut],\nTitta K. Kotilainen [ctb]",
  "Maintainer": "Pedro J. Aphalo <pedro.aphalo@helsinki.fi>",
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  "_created": "2026-10-18T01:19:12.000Z",
  "_published": "2026-10-18T01:26:51.117Z",
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    "author": "Pedro Aphalo <pedro.aphalo@helsinki.fi>",
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      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "inst.sn",
        "name",
        "calib.date",
        "start.date",
        "end.date",
        "coeffs.file"
      ],
      "rows": 1,
      "table": true,
      "tojson": true
    },
    {
      "name": "FLMS04133_descriptors",
      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "FLMS04133_none.mthd",
      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "FLMS04133_simple.mthd",
      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "FLMS04133_sun.mthd",
      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "FLMS04133_ylianttila.mthd",
      "title": "Flame S spectrometer s/n FLMS04133",
      "object": "calibs-FLMS04133",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "halogen.raw_mspct",
      "title": "Raw counts data for a lamp measurement.",
      "object": "raw-counts",
      "class": [
        "raw_mspct",
        "generic_mspct",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "JAZA3098_calib_dates.df",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "inst.sn",
        "name",
        "calib.date",
        "start.date",
        "end.date",
        "coeffs.file"
      ],
      "rows": 1,
      "table": true,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch1_descriptors",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch1_none.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch1_simple.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch1_sun.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch1_ylianttila.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch2_descriptors",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch2_none.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch2_simple.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch2_sun.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "JAZA3098_ch2_ylianttila.mthd",
      "title": "Jaz spectrometer s/n JAZA3098",
      "object": "calibs-JAZA3098",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP11278_calib_dates.df",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "inst.sn",
        "diffuser",
        "name",
        "calib.date",
        "start.date",
        "end.date",
        "coeffs.file",
        "diffuser.file"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP11278_descriptors",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP11278_none.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP11278_short_flt_ref.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP11278_simple.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP11278_sun.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP11278_ylianttila.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP11278",
      "object": "calibs-MAYP11278",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP112785_calib_dates.df",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "inst.sn",
        "diffuser",
        "name",
        "calib.date",
        "start.date",
        "end.date",
        "coeffs.file",
        "diffuser.file"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP112785_descriptors",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP112785_none.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP112785_simple.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP112785_sun.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP112785_ylianttila.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP112785",
      "object": "calibs-MAYP112785",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP114590_cal.spct",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "calibration_spct",
        "generic_spct",
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "w.length",
        "irrad.mult"
      ],
      "rows": 2068,
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP114590_calib_dates.df",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "inst.sn",
        "name",
        "calib.date",
        "start.date",
        "end.date",
        "coeffs.file",
        "diffuser.file"
      ],
      "rows": 1,
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP114590_descriptors",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP114590_none.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP114590_simple.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MAYP114590_sun.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "MAYP114590_ylianttila.mthd",
      "title": "Maya2000 Pro spectrometer s/n MAYP114590",
      "object": "calibs-MAYP114590",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "red_filter.raw_mspct",
      "title": "Raw counts data for a filter measurement",
      "object": "raw-counts",
      "class": [
        "raw_mspct",
        "generic_mspct",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "sun001.raw_mspct",
      "title": "Raw counts data for a lamp measurement.",
      "object": "raw-counts",
      "class": [
        "raw_mspct",
        "generic_mspct",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "white_grow_LED.raw_mspct",
      "title": "Raw counts data for a lamp measurement.",
      "object": "raw-counts",
      "class": [
        "raw_mspct",
        "generic_mspct",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "xenon_flash.raw_mspct",
      "title": "Raw counts data for a lamp measurement.",
      "object": "raw-counts",
      "class": [
        "raw_mspct",
        "generic_mspct",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ooacquire-package",
      "title": "ooacquire: Acquire Data from Ocean Optics Spectrometers",
      "topics": [
        "ooacquire-package",
        "ooacquire"
      ]
    },
    {
      "page": "acq_fraction_interactive",
      "title": "Acquire spectral fraction",
      "concept": [
        "interactive acquisition functions"
      ],
      "topics": [
        "acq_fraction_interactive"
      ]
    },
    {
      "page": "acq_irrad_interactive",
      "title": "Acquire spectral irradiance or spectral fluence",
      "concept": [
        "interactive acquisition functions"
      ],
      "topics": [
        "acq_irrad_interactive"
      ]
    },
    {
      "page": "acq_raw_mspct",
      "title": "Take one set of spectral readings",
      "concept": [
        "raw-counts-spectra acquisition functions"
      ],
      "topics": [
        "acq_raw_mspct"
      ]
    },
    {
      "page": "acq_raw_spct",
      "title": "Measure one raw spectrum",
      "concept": [
        "raw-counts-spectra acquisition functions"
      ],
      "topics": [
        "acq_raw_spct"
      ]
    },
    {
      "page": "acq_settings",
      "title": "Settings for spectral measurement",
      "concept": [
        "acquisition-settings related functions"
      ],
      "topics": [
        "acq_settings",
        "tune_acq_settings"
      ]
    },
    {
      "page": "bleed_nas",
      "title": "Expand NA's to neighbouring pixels",
      "topics": [
        "bleed_nas"
      ]
    },
    {
      "page": "blue_filter.raw_mspct",
      "title": "Raw counts data for a filter measurement",
      "concept": [
        "objects containing example raw-counts data"
      ],
      "topics": [
        "blue_filter.raw_mspct"
      ]
    },
    {
      "page": "check_sn_match",
      "title": "Check consistency of serial number",
      "concept": [
        "spectral data-processing functions"
      ],
      "topics": [
        "check_sn_match"
      ]
    },
    {
      "page": "choose_ch_interactive",
      "title": "Interactively select a channel",
      "concept": [
        "interactive acquisition utility functions"
      ],
      "topics": [
        "choose_ch_interactive"
      ]
    },
    {
      "page": "choose_sr_interactive",
      "title": "Interactively select an instrument",
      "concept": [
        "interactive acquisition utility functions"
      ],
      "topics": [
        "choose_sr_interactive"
      ]
    },
    {
      "page": "collect_spct_files",
      "title": "Collect spectra into a collection",
      "concept": [
        "functions for importing spectral data from files"
      ],
      "topics": [
        "collect_spct_files"
      ]
    },
    {
      "page": "compute_irrad_calibration",
      "title": "Compute calibration multipliers.",
      "topics": [
        "compute_irrad_calibration"
      ]
    },
    {
      "page": "end_session",
      "title": "Disconnect from spectrometer",
      "concept": [
        "spectrometer-connection functions"
      ],
      "topics": [
        "end_session"
      ]
    },
    {
      "page": "example-scripts",
      "title": "Data acquisition scripts",
      "topics": [
        "data-acquisition-scripts"
      ]
    },
    {
      "page": "f.trigger.message",
      "title": "Manual trigger request",
      "concept": [
        "interactive acquisition utility functions"
      ],
      "topics": [
        "f.trigger.message"
      ]
    },
    {
      "page": "files_rm_jwrapper",
      "title": "Remove Java wrapper from objects in files",
      "concept": [
        "Functions and methods related to instrument descriptors."
      ],
      "topics": [
        "files_rm_jwrapper"
      ]
    },
    {
      "page": "files_s_irrad_update",
      "title": "Recompute spectral irradiance in objects in files",
      "concept": [
        "Functions and methods related to instrument descriptors."
      ],
      "topics": [
        "files_s_irrad_update"
      ]
    },
    {
      "page": "filter_correction",
      "title": "Correct for stray light",
      "topics": [
        "filter_correction",
        "no_filter_correction"
      ]
    },
    {
      "page": "find_spct_names",
      "title": "Find names of raw-counts members",
      "topics": [
        "find_spct_names"
      ]
    },
    {
      "page": "FLMS00416_descriptors",
      "title": "Flame S spectrometer s/n FLMS00416",
      "concept": [
        "objects containing instrument-specific data"
      ],
      "topics": [
        "FLMS00416_cal.spct",
        "FLMS00416_calib_dates.df",
        "FLMS00416_descriptors",
        "FLMS00416_none.mthd",
        "FLMS00416_simple.mthd",
        "FLMS00416_sun.mthd",
        "FLMS00416_ylianttila.mthd"
      ]
    },
    {
      "page": "FLMS00440_descriptors",
      "title": "Flame S spectrometer s/n FLMS00440",
      "concept": [
        "objects containing instrument-specific data"
      ],
      "topics": [
        "FLMS00440_cal.spct",
        "FLMS00440_calib_dates.df",
        "FLMS00440_descriptors",
        "FLMS00440_none.mthd",
        "FLMS00440_simple.mthd",
        "FLMS00440_sun.mthd",
        "FLMS00440_ylianttila.mthd"
      ]
    },
    {
      "page": "FLMS00673_descriptors",
      "title": "Flame S spectrometer s/n FLMS00673",
      "concept": [
        "objects containing instrument-specific data"
      ],
      "topics": [
        "FLMS00673_cal.spct",
        "FLMS00673_calib_dates.df",
        "FLMS00673_descriptors",
        "FLMS00673_none.mthd",
        "FLMS00673_simple.mthd",
        "FLMS00673_sun.mthd",
        "FLMS00673_ylianttila.mthd"
      ]
    },
    {
      "page": "FLMS04133_descriptors",
      "title": "Flame S spectrometer s/n FLMS04133",
      "concept": [
        "objects containing instrument-specific data"
      ],
      "topics": [
        "FLMS04133_cal.spct",
        "FLMS04133_calib_dates.df",
        "FLMS04133_descriptors",
        "FLMS04133_none.mthd",
        "FLMS04133_simple.mthd",
        "FLMS04133_sun.mthd",
        "FLMS04133_ylianttila.mthd"
      ]
    },
    {
      "page": "foreign-files",
      "title": "Example foreign data files",
      "topics": [
        "foreign-data-files"
      ]
    },
    {
      "page": "get_oo_descriptor",
      "title": "Get the instrument description and EEPROM data",
      "concept": [
        "Functions and methods related to instrument descriptors"
      ],
      "topics": [
        "get_oo_descriptor"
      ]
    },
    {
      "page": "get_oo_settings",
      "title": "Get the current values of instrument settings",
      "concept": [
        "Functions and methods for instrument settings"
      ],
      "topics": [
        "get_oo_settings"
      ]
    },
    {
      "page": "halogen.raw_mspct",
      "title": "Raw counts data for a lamp measurement.",
      "concept": [
        "objects containing example raw-counts data"
      ],
      "topics": [
        "halogen.raw_mspct"
      ]
    },
    {
      "page": "hs_acq_raw_mspct",
      "title": "Acquire spectra at high speed",
      "concept": [
        "raw-counts-spectra acquisition functions"
      ],
      "topics": [
        "hs_acq_raw_mspct"
      ]
    },
    {
      "page": "instr_defaults",
      "title": "Fetch spectrometer defaults",
      "concept": [
        "Functions and methods related to instrument descriptors."
      ],
      "topics": [
        "default_descriptor",
        "default_method",
        "instr_defaults"
      ]
    },
    {
      "page": "irrad_summary_table",
      "title": "Summarize spectral irradiance or fluence",
      "topics": [
        "irrad_summary_table"
      ]
    },
    {
      "page": "JAZA3098_descriptors",
      "title": "Jaz spectrometer s/n JAZA3098",
      "concept": [
        "objects containing instrument-specific data"
      ],
      "topics": [
        "JAZA3098_calib_dates.df",
        "JAZA3098_ch1_descriptors",
        "JAZA3098_ch1_none.mthd",
        "JAZA3098_ch1_simple.mthd",
        "JAZA3098_ch1_sun.mthd",
        "JAZA3098_ch1_ylianttila.mthd",
        "JAZA3098_ch2_descriptors",
        "JAZA3098_ch2_none.mthd",
        "JAZA3098_ch2_simple.mthd",
        "JAZA3098_ch2_sun.mthd",
        "JAZA3098_ch2_ylianttila.mthd",
        "JAZA3098_descriptors"
      ]
    },
    {
      "page": "linearize_counts",
      "title": "Function to apply linearization correction to raw counts data.",
      "concept": [
        "spectral data-processing functions"
      ],
      "topics": [
        "linearize_counts"
      ]
    },
    {
      "page": "list_instruments",
      "title": "List connected spectrometers",
      "concept": [
        "spectrometer-connection functions"
      ],
      "topics": [
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