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Scrape and Analyze Wikipedia & Trait Data for a Species

Source: R/get_trait_data.R
get_trait_data.Rd

Given a binomial species name, this function retrieves optional metadata from Wikipedia (taxonomic summary, taxonomy, image, and a color palette) and joins relevant plant/trait data from a TRY-style or user-provided trait table. Fuzzy matching is used for both TRY and local tables to handle minor spelling or naming mismatches.

Usage

get_trait_data(
  species,
  remove_bg = FALSE,
  do_palette = TRUE,
  do_taxonomy = TRUE,
  do_summary = TRUE,
  do_image = TRUE,
  bg_thresh = 80,
  green_delta = 20,
  n_palette = 5,
  preview = FALSE,
  save_folder = NULL,
  use_try = FALSE,
  try_data = NULL,
  trait_species_col = "AccSpeciesName",
  local_trait_df = NULL,
  local_species_col = "species",
  max_dist = 1
)

Arguments

species

Character. Species name (binomial, e.g. "Acacia karroo").

remove_bg

Logical. If TRUE, call remove.bg via remove_bg_and_save() to remove the background from the Wikipedia infobox image and use the processed PNG for preview/palette. Default: FALSE.

do_palette, do_taxonomy, do_summary, do_image

Logical. Control which metadata to scrape. All default to TRUE.

bg_thresh

Integer. Deprecated/ignored when remove_bg = TRUE. Kept for signature compatibility. Default: 80.

green_delta

Integer. Deprecated/ignored when remove_bg = TRUE. Kept for signature compatibility. Default: 20.

n_palette

Integer. Number of colors to extract for the palette. Default: 5.

preview

Logical. Print the processed image (magick) in the console. Default: FALSE.

save_folder

Character or NULL. If non-NULL, write the PNG used for palette/preview into this folder. When remove_bg = TRUE, the background-removed PNG is written here; otherwise the original image is written. If NULL and remove_bg = TRUE, a temporary directory is used.

use_try

Logical. If TRUE, join plant traits using a TRY-format database/table. Default: FALSE.

try_data

Character (path) or data.frame. Path to a TRY file, or a data frame containing TRY-style trait data (must include trait_species_col, TraitName, and OrigValueStr).

trait_species_col

Name of the species column in the TRY trait table. Default: "AccSpeciesName".

local_trait_df

Optional. data.frame of local trait data (any wide table). All columns except the species column are returned.

local_species_col

Name of the species column in the local trait table. Default: "species".

max_dist

Numeric. Maximum distance for fuzzy matching (Jaro–Winkler via fuzzyjoin::stringdist_left_join). Default: 1.

Value

A tibble (one row) with columns: species, optional metadata (summary, taxonomy ranks, img_url, palette, image_file), and all available trait columns found via TRY/local joins. image_file contains the normalized path to the PNG used for palette/preview (or NA if none).

Details

When remove_bg = TRUE, the infobox image background is removed using the remove.bg API via an internal helper (remove_bg_and_save()), the resulting PNG is re-read with magick, and the palette is extracted from that processed image. Set the environment variable REMOVE_BG_API_KEY to a valid remove.bg API key before calling.

  • Wikipedia: summary via REST API; taxonomy parsed from the infobox.

  • Image: first infobox image is used; when remove_bg = TRUE the function calls the remove.bg API. Set Sys.setenv(REMOVE_BG_API_KEY = "…").

  • Palette: simple k-means on non-transparent pixels of the (processed) PNG.

  • Traits (TRY): wide table produced from TraitName and numeric OrigValueStr.

  • Traits (local): returns all columns except the species column.

  • Dependencies: dplyr, purrr, tibble, fuzzyjoin, rvest, httr, stringr, jsonlite, magick, abind.

Examples

if (FALSE) { # \dontrun{
# Using TRY table
get_trait_data("Acacia karroo",
               use_try = TRUE,
               try_data = try_traits,
               trait_species_col = "SpeciesName")

# Using a local trait table
get_trait_data("Acraea horta", local_trait_df = traits, local_species_col = "species")

# Metadata only, with background removal and saving to a folder
Sys.setenv(REMOVE_BG_API_KEY = "<your-removebg-key>")
get_trait_data("Acacia karroo", use_try = FALSE, remove_bg = TRUE, save_folder = "out/")
} # }