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      "title": "Estimate density & abundance",
      "topics": [
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    {
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      "title": "Relative trackline detection probabilities from Barlow (2015).",
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      "title": "Cruise data processed for the CNP, 1986 - 2020 (150 km segment lengths)",
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      "title": "Example of coded edits to 'cruz' object.",
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      "title": "Apply edits to a 'DAS' file...",
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      "title": "Edit 'DAS' files and save edited versions",
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    {
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      "title": "Use a 'Shiny' app to explore a 'DAS' file and build up a list of edits. Those edits will be saved as a list of instructions, which can subsequently be provided as an argument to 'LTabundR::process_surveys()', which will apply your list of edits before processing the data. This framework allows you to record details of required edits reproducibly without ever modifying the original dataset or producing modified versions of the original.",
      "topics": [
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    {
      "page": "das_interpolate",
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      "title": "Read in and process a 'DAS' file",
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      "page": "das_readtext",
      "title": "Read DAS file without parsing columns",
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    {
      "page": "das_time",
      "title": "Adjust the timestamp within a 'DAS' file",
      "topics": [
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    {
      "page": "df_curve",
      "title": "Get detection function curve",
      "topics": [
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    {
      "page": "df_fit",
      "title": "Fit a detection function to 'WinCruz' data",
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    {
      "page": "df_plot",
      "title": "Plot the best-fit detection function model(s)",
      "topics": [
        "df_plot"
      ]
    },
    {
      "page": "eez",
      "title": "EEZ (all US EEZ boundaries)",
      "topics": [
        "eez"
      ]
    },
    {
      "page": "eez_ccs",
      "title": "EEZ - California Current System (formatted for sf / tmap mapping)",
      "topics": [
        "eez_ccs"
      ]
    },
    {
      "page": "eez_hawaii",
      "title": "EEZ - Hawaii (formatted for sf / tmap mapping)",
      "topics": [
        "eez_hawaii"
      ]
    },
    {
      "page": "er_simulator",
      "title": "Encounter Rate simulator test",
      "topics": [
        "er_simulator"
      ]
    },
    {
      "page": "example_cruz",
      "title": "Example cruz object (WHICEAS 2020)",
      "topics": [
        "example_cruz"
      ]
    },
    {
      "page": "example_settings",
      "title": "Example settings used in 'LTabundR' vignette (WHICEAS 2020)",
      "topics": [
        "example_settings"
      ]
    },
    {
      "page": "filter_cohort",
      "title": "Filter segments & sightings for a single cohort by species/region/year, etc.",
      "topics": [
        "filter_cohort"
      ]
    },
    {
      "page": "filter_cruz",
      "title": "Filter 'cruz' objects by species/region/year, etc.",
      "topics": [
        "filter_cruz"
      ]
    },
    {
      "page": "g0_combine",
      "title": "Combine estimates of weighted g(0) and its CV",
      "topics": [
        "g0_combine"
      ]
    },
    {
      "page": "g0_model",
      "title": "Estimate relative g(0) in different survey conditions",
      "topics": [
        "g0_model"
      ]
    },
    {
      "page": "g0_optimize",
      "title": "Find g0 values Nelder-Mead using optimization",
      "topics": [
        "g0_optimize"
      ]
    },
    {
      "page": "g0_plot",
      "title": "Plot Rg(0) curves",
      "topics": [
        "g0_plot"
      ]
    },
    {
      "page": "g0_results",
      "title": "Relative trackline detection probabilities - Rg(0)",
      "topics": [
        "g0_results"
      ]
    },
    {
      "page": "g0_table",
      "title": "Compile table of Relative g(0) estimates by Beaufort state",
      "topics": [
        "g0_table"
      ]
    },
    {
      "page": "g0_weighted",
      "title": "Find a single weighted g(0) estimate (and CV) from a set of Beaufort-specific estimates.",
      "topics": [
        "g0_weighted"
      ]
    },
    {
      "page": "gg_effort",
      "title": "Add 'cruz' effort to a base 'ggplot2' map.",
      "topics": [
        "gg_effort"
      ]
    },
    {
      "page": "gg_geostratum",
      "title": "Add 'cruz' geostrata to a base 'ggplot2' map.",
      "topics": [
        "gg_geostratum"
      ]
    },
    {
      "page": "gg_sightings",
      "title": "Add 'cruz' sightings to a base 'ggplot2' map.",
      "topics": [
        "gg_sightings"
      ]
    },
    {
      "page": "ggplot_idl",
      "title": "Modify a 'ggplot' object to handle the International Date Line (IDL)",
      "topics": [
        "ggplot_idl"
      ]
    },
    {
      "page": "group_size",
      "title": "Group size estimation wrapper",
      "topics": [
        "group_size"
      ]
    },
    {
      "page": "group_size_calibration",
      "title": "Group size calibration",
      "topics": [
        "group_size_calibration"
      ]
    },
    {
      "page": "group_size_coefficients",
      "title": "Group size coefficients",
      "topics": [
        "group_size_coefficients"
      ]
    },
    {
      "page": "idl_coerce",
      "title": "Coerce eastern longitudes to western (i.e., less than - 180)",
      "topics": [
        "idl_coerce"
      ]
    },
    {
      "page": "land",
      "title": "Land",
      "topics": [
        "land"
      ]
    },
    {
      "page": "load_cohort_settings",
      "title": "Load cohort-specific settings",
      "topics": [
        "load_cohort_settings"
      ]
    },
    {
      "page": "load_settings",
      "title": "Load settings for processing 'WinCruz' surveys",
      "topics": [
        "load_settings"
      ]
    },
    {
      "page": "load_survey_settings",
      "title": "Load survey settings",
      "topics": [
        "load_survey_settings"
      ]
    },
    {
      "page": "lta",
      "title": "Line transect analysis",
      "topics": [
        "lta"
      ]
    },
    {
      "page": "lta_checks",
      "title": "Check for missing data before running 'lta()'.",
      "topics": [
        "lta_checks"
      ]
    },
    {
      "page": "lta_ci",
      "title": "Compute confidence intervals of a bootstrapped LTA estimate",
      "topics": [
        "lta_ci"
      ]
    },
    {
      "page": "lta_combine",
      "title": "Combine LTA estimates from separate regions",
      "topics": [
        "lta_combine"
      ]
    },
    {
      "page": "lta_delta_method",
      "title": "Estimate CV and 95% confidence intervals with the delta method",
      "topics": [
        "lta_delta_method"
      ]
    },
    {
      "page": "lta_destratify",
      "title": "Pool stratified LTA results",
      "topics": [
        "lta_destratify"
      ]
    },
    {
      "page": "lta_diagnostics",
      "title": "Run diagnostics on a LTA result",
      "topics": [
        "lta_diagnostics"
      ]
    },
    {
      "page": "lta_enlist",
      "title": "Compile a directory of LTA results into a list",
      "topics": [
        "lta_enlist"
      ]
    },
    {
      "page": "lta_estimates",
      "title": "Build a function that creates 'estimates' sub-lists for 'lta()'",
      "topics": [
        "lta_estimates"
      ]
    },
    {
      "page": "lta_plot",
      "title": "Plot LTA results",
      "topics": [
        "lta_plot"
      ]
    },
    {
      "page": "lta_pool",
      "title": "Pool bootstraps from multiple 'lta()' outputs",
      "topics": [
        "lta_pool"
      ]
    },
    {
      "page": "lta_report",
      "title": "Build LTA tables for standard reports",
      "topics": [
        "lta_report"
      ]
    },
    {
      "page": "lta_result",
      "title": "Example of LTA results for three delphinids in 2010 and 2017",
      "topics": [
        "lta_result"
      ]
    },
    {
      "page": "lta_subgroup",
      "title": "Subgroup-based line transect analysis",
      "topics": [
        "lta_subgroup"
      ]
    },
    {
      "page": "map_cruz",
      "title": "Interactive map for 'Wincruz' survey",
      "topics": [
        "map_cruz"
      ]
    },
    {
      "page": "noaa_10km_1986_2020",
      "title": "Cruise data processed for all NOAA SWFSC and PIFSC surveys, 1986 - 2020 (10 km segment lengths)",
      "topics": [
        "noaa_10km_1986_2020"
      ]
    },
    {
      "page": "points_to_line",
      "title": "Convert coordinates to a 'sf' line",
      "topics": [
        "points_to_line"
      ]
    },
    {
      "page": "prep_bootstrap_datasets",
      "title": "Prepare bootstrapped versions of datasets",
      "topics": [
        "prep_bootstrap_datasets"
      ]
    },
    {
      "page": "process_km",
      "title": "Calculate distances between rows in a DAS file",
      "topics": [
        "process_km"
      ]
    },
    {
      "page": "process_polygon",
      "title": "Format a CSV into a polygon for mapping",
      "topics": [
        "process_polygon"
      ]
    },
    {
      "page": "process_sightings",
      "title": "Process survey sightings",
      "topics": [
        "process_sightings"
      ]
    },
    {
      "page": "process_strata",
      "title": "Process geo-strata",
      "topics": [
        "process_strata"
      ]
    },
    {
      "page": "process_subgroups",
      "title": "Analyze subgroup detections for false killer whales",
      "topics": [
        "process_subgroups"
      ]
    },
    {
      "page": "process_surveys",
      "title": "Process & prepare 'Wincruz' survey data for analysis.",
      "topics": [
        "process_surveys"
      ]
    },
    {
      "page": "read_polygon",
      "title": "Read in a DAT file with polygon(s)",
      "topics": [
        "read_polygon"
      ]
    },
    {
      "page": "region_das",
      "title": "Find DAS rows occurring within a region / regions",
      "topics": [
        "region_das"
      ]
    },
    {
      "page": "region_segments",
      "title": "Find segments occurring within a region / regions",
      "topics": [
        "region_segments"
      ]
    },
    {
      "page": "segmentize",
      "title": "Segmentize survey effort",
      "topics": [
        "segmentize"
      ]
    },
    {
      "page": "ships",
      "title": "Ship codes",
      "topics": [
        "ships"
      ]
    },
    {
      "page": "species_codes",
      "title": "Species codes used in WinCRUZ",
      "topics": [
        "species_codes"
      ]
    },
    {
      "page": "species_translator",
      "title": "Species name/code search engine",
      "topics": [
        "species_translator"
      ]
    },
    {
      "page": "strata_area",
      "title": "Combine geostrata and compute area",
      "topics": [
        "strata_area"
      ]
    },
    {
      "page": "strata_ccs",
      "title": "Strata CCS",
      "topics": [
        "strata_ccs"
      ]
    },
    {
      "page": "strata_cnp",
      "title": "Strata CNP",
      "topics": [
        "strata_cnp"
      ]
    },
    {
      "page": "strata_etp",
      "title": "Strata ETP",
      "topics": [
        "strata_etp"
      ]
    },
    {
      "page": "strata_explore",
      "title": "Explore the package's strata polygon gallery",
      "topics": [
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      ]
    },
    {
      "page": "strata_segments",
      "title": "Display/map stratum assignments for segments",
      "topics": [
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      ]
    },
    {
      "page": "strata_select",
      "title": "Select strata polygons for standard survey regions",
      "topics": [
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    },
    {
      "page": "subgroup_edits",
      "title": "Stage edits to subgroups (e.g., phase and population assignments)",
      "topics": [
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      ]
    },
    {
      "page": "subgroup_events",
      "title": "Find subgroup size estimates within a DAS file",
      "topics": [
        "subgroup_events"
      ]
    },
    {
      "page": "subgroup_explorer",
      "title": "Simple explorer for subgroups data",
      "topics": [
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    },
    {
      "page": "subgroup_phases",
      "title": "Review & stage edits to subgroup phase assignments",
      "topics": [
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    {
      "page": "subgroup_populations",
      "title": "Assign subgroups to populations based on polygons",
      "topics": [
        "subgroup_populations"
      ]
    },
    {
      "page": "subgroup_sightings",
      "title": "Summarize sightings (for subgroup species) based on subgroups",
      "topics": [
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    },
    {
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      "title": "Summarize 'Wincruz' by Beaufort Sea State",
      "topics": [
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    },
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      "page": "summarize_distances",
      "title": "Summarize sighting distances in a table",
      "topics": [
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      "page": "summarize_effort",
      "title": "Summarize 'Wincruz' survey effort",
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      "title": "Inventory sightings and species counts from a 'Wincruz' survey",
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    },
    {
      "page": "summarize_species",
      "title": "Summarize sightings for a species (or several)",
      "topics": [
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      "buildurl": "https://github.com/r-universe/pifsc-protected-species-division/actions/runs/29532703967"
    }
  ]
}