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  "Title": "Retrieving, Organizing, and Analyzing Estuary Monitoring Data",
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  "Date": "2025-02-02",
  "Author": "Marcus W. Beck [aut, cre], Kimberly Cressman [ctb]",
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  "Description": "Tools for retrieving, organizing, and analyzing\nenvironmental data from the System Wide Monitoring Program of\nthe National Estuarine Research Reserve System\n<https://cdmo.baruch.sc.edu/>. These tools address common\nchallenges associated with continuous time series data for\nenvironmental decision making.",
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    "decomp",
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    "param_names",
    "parser",
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    "plot_quants",
    "plot_summary",
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    "qaqc",
    "qaqcchk",
    "rem_reps",
    "setstep",
    "single_param",
    "site_codes",
    "site_codes_ind",
    "smoother",
    "swmpr",
    "time_vec"
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      "name": "apacpnut",
      "title": "Example nutrient data for Apalachicola Bay Cat Point station.",
      "object": "apacpnut",
      "class": [
        "swmpr",
        "data.frame"
      ],
      "fields": [
        "datetimestamp",
        "po4f",
        "f_po4f",
        "nh4f",
        "f_nh4f",
        "no2f",
        "f_no2f",
        "no3f",
        "f_no3f",
        "no23f",
        "f_no23f",
        "chla_n",
        "f_chla_n"
      ],
      "rows": 215,
      "table": true,
      "tojson": true
    },
    {
      "name": "apacpwq",
      "title": "Example water quality data for Apalachicola Bay Cat Point station.",
      "object": "apacpwq",
      "class": [
        "swmpr",
        "data.frame"
      ],
      "fields": [
        "datetimestamp",
        "temp",
        "f_temp",
        "spcond",
        "f_spcond",
        "sal",
        "f_sal",
        "do_pct",
        "f_do_pct",
        "do_mgl",
        "f_do_mgl",
        "depth",
        "f_depth",
        "cdepth",
        "f_cdepth",
        "level",
        "f_level",
        "clevel",
        "f_clevel",
        "ph",
        "f_ph",
        "turb",
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        "f_chlfluor"
      ],
      "rows": 70176,
      "table": true,
      "tojson": true
    },
    {
      "name": "apadbwq",
      "title": "Example water quality data for Apalachicola Bay Dry Bar station.",
      "object": "apadbwq",
      "class": [
        "swmpr",
        "data.frame"
      ],
      "fields": [
        "datetimestamp",
        "temp",
        "f_temp",
        "spcond",
        "f_spcond",
        "sal",
        "f_sal",
        "do_pct",
        "f_do_pct",
        "do_mgl",
        "f_do_mgl",
        "depth",
        "f_depth",
        "cdepth",
        "f_cdepth",
        "level",
        "f_level",
        "clevel",
        "f_clevel",
        "ph",
        "f_ph",
        "turb",
        "f_turb",
        "chlfluor",
        "f_chlfluor"
      ],
      "rows": 70176,
      "table": true,
      "tojson": true
    },
    {
      "name": "apaebmet",
      "title": "Example weather data for Apalachicola Bay East Bay station.",
      "object": "apaebmet",
      "class": [
        "swmpr",
        "data.frame"
      ],
      "fields": [
        "datetimestamp",
        "atemp",
        "f_atemp",
        "rh",
        "f_rh",
        "bp",
        "f_bp",
        "wspd",
        "f_wspd",
        "maxwspd",
        "f_maxwspd",
        "wdir",
        "f_wdir",
        "sdwdir",
        "f_sdwdir",
        "totpar",
        "f_totpar",
        "totprcp",
        "f_totprcp",
        "cumprcp",
        "f_cumprcp",
        "totsorad",
        "f_totsorad"
      ],
      "rows": 70176,
      "table": true,
      "tojson": true
    },
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      "object": "stat_locs",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
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        "latitude",
        "longitude",
        "gmt_off"
      ],
      "rows": 178,
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "aggremetab",
      "title": "Aggregate metabolism data",
      "concept": [
        "analyze"
      ],
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        "aggremetab",
        "aggremetab.swmpr"
      ]
    },
    {
      "page": "aggreswmp",
      "title": "Aggregate swmpr data",
      "concept": [
        "analyze"
      ],
      "topics": [
        "aggreswmp",
        "aggreswmp.swmpr"
      ]
    },
    {
      "page": "all_params",
      "title": "Import current station records from the CDMO",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "all_params"
      ]
    },
    {
      "page": "all_params_dtrng",
      "title": "Get CDMO records within a date range",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "all_params_dtrng"
      ]
    },
    {
      "page": "apacpnut",
      "title": "Example nutrient data for Apalachicola Bay Cat Point station.",
      "topics": [
        "apacpnut"
      ]
    },
    {
      "page": "apacpwq",
      "title": "Example water quality data for Apalachicola Bay Cat Point station.",
      "topics": [
        "apacpwq"
      ]
    },
    {
      "page": "apadbwq",
      "title": "Example water quality data for Apalachicola Bay Dry Bar station.",
      "topics": [
        "apadbwq"
      ]
    },
    {
      "page": "apaebmet",
      "title": "Example weather data for Apalachicola Bay East Bay station.",
      "topics": [
        "apaebmet"
      ]
    },
    {
      "page": "calckl",
      "title": "Calculate oxygen mass transfer coefficient",
      "topics": [
        "calckl"
      ]
    },
    {
      "page": "cens_id",
      "title": "Flag observations above/below detection limits",
      "concept": [
        "organize"
      ],
      "topics": [
        "cens_id",
        "cens_id.swmpr"
      ]
    },
    {
      "page": "comb",
      "title": "Combine swmpr data",
      "concept": [
        "organize"
      ],
      "topics": [
        "comb",
        "comb.default",
        "comb.swmpr"
      ]
    },
    {
      "page": "decomp",
      "title": "Simple trend decomposition",
      "concept": [
        "analyze"
      ],
      "topics": [
        "decomp",
        "decomp.default",
        "decomp.swmpr"
      ]
    },
    {
      "page": "decomp_cj",
      "title": "Simple trend decomposition of monthly swmpr data",
      "concept": [
        "analyze"
      ],
      "topics": [
        "decomp_cj",
        "decomp_cj.default",
        "decomp_cj.swmpr"
      ]
    },
    {
      "page": "decompTs",
      "title": "Decompose a time series",
      "topics": [
        "decompTs"
      ]
    },
    {
      "page": "ecometab",
      "title": "Ecosystem metabolism",
      "concept": [
        "analyze"
      ],
      "topics": [
        "ecometab",
        "ecometab.default",
        "ecometab.swmpr"
      ]
    },
    {
      "page": "gradcols",
      "title": "Get colors for plots",
      "topics": [
        "gradcols"
      ]
    },
    {
      "page": "hist.swmpr",
      "title": "Plot swmpr using a histogram",
      "concept": [
        "analyze"
      ],
      "topics": [
        "hist.swmpr"
      ]
    },
    {
      "page": "import_local",
      "title": "Import local CDMO data",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "import_local"
      ]
    },
    {
      "page": "map_reserve",
      "title": "Map a reserve",
      "concept": [
        "analyze"
      ],
      "topics": [
        "map_reserve"
      ]
    },
    {
      "page": "metab_day",
      "title": "Identify metabolic days in a time series",
      "topics": [
        "metab_day",
        "metab_day.default"
      ]
    },
    {
      "page": "na.approx.swmpr",
      "title": "Linearly interpolate gaps",
      "concept": [
        "analyze"
      ],
      "topics": [
        "na.approx.swmpr"
      ]
    },
    {
      "page": "overplot",
      "title": "Plot multiple SWMP time series on the same y-axis",
      "concept": [
        "analyze"
      ],
      "topics": [
        "overplot",
        "overplot.default",
        "overplot.swmpr"
      ]
    },
    {
      "page": "oxySol",
      "title": "Dissolved oxygen at saturation",
      "topics": [
        "oxySol"
      ]
    },
    {
      "page": "param_names",
      "title": "Get parameters of a given type",
      "topics": [
        "param_names"
      ]
    },
    {
      "page": "parser",
      "title": "Parse web results for swmpr",
      "topics": [
        "parser"
      ]
    },
    {
      "page": "plot_metab",
      "title": "Plot ecosystem metabolism for a swmpr object",
      "concept": [
        "analyze"
      ],
      "topics": [
        "plot_metab",
        "plot_metab.swmpr"
      ]
    },
    {
      "page": "plot_quants",
      "title": "Create a plot of data for a single year overlaid on historical data.",
      "concept": [
        "analyze"
      ],
      "topics": [
        "plot_quants",
        "plot_quants.swmpr"
      ]
    },
    {
      "page": "plot_summary",
      "title": "Plot graphical summaries of SWMP data",
      "concept": [
        "analyze"
      ],
      "topics": [
        "plot_summary",
        "plot_summary.swmpr"
      ]
    },
    {
      "page": "plot_wind",
      "title": "Create a wind rose",
      "concept": [
        "analyze"
      ],
      "topics": [
        "plot_wind",
        "plot_wind.swmpr"
      ]
    },
    {
      "page": "plot.swmpr",
      "title": "Plot swmpr data",
      "concept": [
        "analyze"
      ],
      "topics": [
        "lines.swmpr",
        "plot.swmpr"
      ]
    },
    {
      "page": "qaqc",
      "title": "QAQC filtering for SWMP data",
      "concept": [
        "organize"
      ],
      "topics": [
        "qaqc",
        "qaqc.swmpr"
      ]
    },
    {
      "page": "qaqcchk",
      "title": "Summary of QAQC flags in SWMP data",
      "concept": [
        "organize"
      ],
      "topics": [
        "qaqcchk",
        "qaqcchk.swmpr"
      ]
    },
    {
      "page": "rem_reps",
      "title": "Remove replicates in nutrient data",
      "concept": [
        "organize"
      ],
      "topics": [
        "rem_reps",
        "rem_reps.swmpr"
      ]
    },
    {
      "page": "setstep",
      "title": "Format a swmpr time vector",
      "concept": [
        "organize"
      ],
      "topics": [
        "setstep",
        "setstep.default",
        "setstep.swmpr"
      ]
    },
    {
      "page": "single_param",
      "title": "Get CDMO records for a single parameter",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "single_param"
      ]
    },
    {
      "page": "site_codes",
      "title": "Obtain metadata for all stations",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "site_codes"
      ]
    },
    {
      "page": "site_codes_ind",
      "title": "Obtain metadata for a single reserve",
      "concept": [
        "retrieve"
      ],
      "topics": [
        "site_codes_ind"
      ]
    },
    {
      "page": "smoother",
      "title": "Smooth swmpr data",
      "concept": [
        "analyze"
      ],
      "topics": [
        "smoother",
        "smoother.default",
        "smoother.swmpr"
      ]
    },
    {
      "page": "stat_locs",
      "title": "Locations of NERRS sites",
      "topics": [
        "stat_locs"
      ]
    },
    {
      "page": "subset.swmpr",
      "title": "Subset a swmpr object",
      "concept": [
        "organize"
      ],
      "topics": [
        "subset.swmpr"
      ]
    },
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