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Create Leaflet map for enriched iNaturalist occurrences

Source: R/functions.R
create_leaflet_occ_map.Rd

[Experimental]

Takes a tibble of iNaturalist occurrences already enriched with species nativeness, IUCN conservation status, EUNIS legal information, and eLTER Standard Observation assignments. Verifies that all required columns are present, builds observation-level HTML popups with linked references to iNaturalist, IUCN Red List, and EUR-Lex directive pages, and returns an interactive Leaflet map with colour-coded markers by iconic taxon group and marker clustering.

Usage

create_leaflet_occ_map(occ_enriched, site_boundary = NULL)

Arguments

occ_enriched

An sf tibble of iNaturalist occurrences enriched with the following columns:

establishmentMeans

list-column of 1 × 2 tibbles with nativeness and authority, produced by add_nativeness_to_occ.

status_IUCN

list-column of N × 4 tibbles with status, authority, name (geographic scope), and url, produced by add_iucn_to_occ.

directive

character. EU directive name, produced by add_eunis_legal_to_occ.

annex

character. EU directive annex, produced by add_eunis_legal_to_occ.

SOBIO_014

logical. Whether the observation contributes to the eLTER Standard Observation SOBIO_014 (Flying insects), assigned by the enrichment pipeline via .assign_eLTER_SOs.

SOBIO_018

logical. Whether the observation contributes to the eLTER Standard Observation SOBIO_018 (Acoustic recording — birds, bats, amphibians, orthoptera), assigned by the enrichment pipeline via .assign_eLTER_SOs.

taxon.id

integer. iNaturalist taxon ID.

name

character. Scientific name.

taxon.preferred_common_name

character. Common name.

taxon.iconic_taxon_name

character. Iconic taxon group (e.g. "Aves", "Plantae") used for marker colouring.

taxon_geoprivacy

character. Geoprivacy status of the taxon ("open", "obscured", "private").

quality_grade

character. iNaturalist data quality grade.

observed_on

Date. Observation date.

public_positional_accuracy

numeric. Positional accuracy in metres.

user.login

character. iNaturalist username of the observer.

uri

character. URL of the iNaturalist observation record.

taxon.default_photo.square_url

character. URL of the taxon thumbnail photo shown in the popup.

site_boundary

An sf object representing the eLTER site boundary polygon, as returned by ReLTER::get_site_info(). If NULL (default), no boundary polygon is drawn on the map.

Value

A leaflet map object with:

  • An OpenStreetMap base tile layer.

  • An optional eLTER site boundary polygon layer.

  • Circle markers for "open" observations (radius 6, full opacity), "obscured" observations (radius 10, reduced opacity), and "unknown" geoprivacy observations (radius 8, low opacity), all with marker clustering enabled.

  • Popups per observation showing:

    • taxon photo, scientific name (linked to iNaturalist), common name, observation date, observer (linked to iNaturalist), and link to the observation record;

    • data quality grade, geoprivacy level, and positional accuracy;

    • IUCN Red List status per geographic scope, with links to the Red List assessments;

    • establishment means and authority, with link to iNaturalist help;

    • EU directive coverage (Habitats and Birds Directives) with links to EUR-Lex;

    • eLTER Standard Observations the record contributes to (SOBIO_014 Flying insects and/or SOBIO_018 Acoustic recording).

  • A legend for iconic taxon groups.

  • A geoprivacy legend control (top right).

  • A layers control to toggle observation groups and site boundary.

Note

Observations with taxon_geoprivacy == "private" are shown on the map with low opacity as their coordinates are approximate.

EU directive links point to the EUR-Lex PDF versions: Birds Directive 2009/147/EC and Habitats Directive 92/43/EEC.

eLTER Standard Observation assignments are based on taxonomic ancestry retrieved from the iNaturalist API. SOBIO_014 covers Insecta; SOBIO_018 covers Aves, Anura, Chiroptera, and Orthoptera. Orthoptera contribute to both SOs simultaneously.

See also

add_iucn_to_occ, add_nativeness_to_occ, add_eunis_legal_to_occ, obs_SO_pie_chart

Author

Alessandro Oggioni, PhD alessandro.oggioni@cnr.it

Examples

if (FALSE) { # \dontrun{
deimsid <- "https://deims.org/6b62feb2-61bf-47e1-b97f-0e909c408db8"
site_boundary <- ReLTER::get_site_info(deimsid = deimsid)

map <- create_leaflet_occ_map(
  occ_enriched  = occ_eLTER_legal,
  site_boundary = site_boundary
)
map
} # }