Class definitions used by camtrapReport to store camera-trap data, report metadata, report sections, and intermediate report objects.
camReport class
The camReport class is the main object class used by camtrapReport. Objects
of this class are usually created with camData(). A camReport object
stores the camera-trap dataset, report metadata, processed summaries, report
modules, status-report modules, and settings used for report generation.
The exported camR object is the low-level Reference Class generator for
advanced use. Calling camR$new() creates an unprepared container; it does
not import data or run the setup and data-status checks performed by
camData(). Use camData() for the normal reporting workflow.
Main fields
Important fields in a camReport object include:
data: A list containing the camera-trap data tables, including observations, deployments, media, locations, sequences, and taxonomy.habitat: Optional habitat information linked to camera locations.study_area: Optional spatial object or path describing the study area.siteName: Name of the study site.title: Title used in the generated report.subtitle: Subtitle used in the generated report.authors: Author or contributor text used in the generated report.institute: Institute or organisation text used in the generated report.description: Study-area or project description used in the generated report.years: Years included in the report summaries.group_definition: Definitions of species or observation groups used in the report.setting: Report settings, including selected focus groups,rem_parameter_scope("pooled"or"annual"),rem_reps,rem_seed, andmap_basemap("offline","cartodb","esri", or"openstreetmap", the default). For noncommercial research reports, the OpenStreetMap mode tries OpenStreetMap Standard, OpenStreetMap Germany, and OpenTopoMap in that order, then a neutral background if all fail. There is no additional eligibility setting. The services' usage terms and visible attributions still apply; no online service guarantees availability. Localfile://reports skip Standard because they cannot send its required web Referer, and start with Germany. Serve the report over HTTP(S) to try Standard first. No header is fabricated."offline"makes no tile requests. Existing explicit CARTO and Esri settings remain subject to their operators' applicable terms. Bundled report modules select their REM scope explicitly; the standard profile is pooled and the EOW profile is annual.data_status: Data-status summaries generated from the input dataset.reportObjectElements: Report modules and related objects used to generate the ecological report.statusReportObjects: Objects used to generate the data-status report.
Supporting classes
camtrapReport also defines supporting classes and class unions used
internally, including camInfo, .Rchunk, .textSection,
characterORnull, characterORlist, characterORlistORnull,
listORnull, and data.frameORnull.
Examples
# Inspect the formal definition of the main report class.
methods::getClass("camReport")
#> Reference Class "camReport":
#>
#> Class fields:
#>
#> Name: data habitat
#> Class: list data.frame
#>
#> Name: data_merged study_area
#> Class: data.frame listORnull
#>
#> Name: siteName title
#> Class: character character
#>
#> Name: subtitle authors
#> Class: character character
#>
#> Name: institute logoPath
#> Class: character character
#>
#> Name: annonator acknowledgement
#> Class: character character
#>
#> Name: description years
#> Class: character numeric
#>
#> Name: group_definition filterExclude
#> Class: list list
#>
#> Name: filterKeep filterCount
#> Class: list numeric
#>
#> Name: filterDuration observed_counts
#> Class: numeric data.frame
#>
#> Name: frequent_species camera_stats
#> Class: data.frame data.frame
#>
#> Name: camera_setup observation_stats
#> Class: data.frame data.frame
#>
#> Name: species_summary species_stats
#> Class: list data.frame
#>
#> Name: species_summary_by_habitat capture
#> Class: data.frame data.frame
#>
#> Name: density_estimates setting
#> Class: data.frame list
#>
#> Name: sun_times packages
#> Class: data.frameORnull character
#>
#> Name: info data_status
#> Class: list list
#>
#> Name: rem .rem_params
#> Class: list list
#>
#> Name: .act_models .any_data_for_rem
#> Class: list logical
#>
#> Name: .tempObjects reportTextElements
#> Class: list list
#>
#> Name: reportObjectElements statusReportObjects
#> Class: list list
#>
#> Name: reportObjects
#> Class: list
#>
#> Class Methods:
#> "get_REM", "get_speciesNames", "get_data_subset", "import", "initFields",
#> "filter", "export", "show#envRefClass", "fit_REM", "getClass", "field",
#> "initialize", "addStatusReportObject", "gui", "get_focus_group",
#> "get_group", "callSuper", "untrace", "setup", "richness",
#> "recetFigTabNumber", "spatial_density", "extractYears", "generateReport",
#> "species_summary_by_location", ".objectPackage", "trace", "getRefClass",
#> "copy", "show", "addReportObject", "usingMethods", "generateStatusReport",
#> "set_focus_group", ".get_REM_Param", "getTableNumber",
#> "add_report_basemap", ".objectParent", "add_group", "getFigureNumber"
#>
#> Reference Superclasses:
#> "envRefClass"
#>
# Check whether the class is registered.
methods::isClass("camReport")
#> [1] TRUE