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Standalone HTML species factsheet with user metadata and photos

Source: R/factsheet.R
factsheet_html.Rd

Builds a single, self-contained HTML file that presents one species as a printable/shareable factsheet - the kind hosted on a supplementary website. It combines two sources of information:

  1. Everything the assessment already computes - range metrics (EOO/AOO and provisional Criterion B category), habitat conversion, fire and protected-area overlap - rendered as a key-metrics grid, the standard charts (composition, protection, and any land-cover / fire time series supplied), a "top anthropic activities" chart derived from the per-class land-cover breakdown, and the interpretive narrative of assessment_report.

  2. Information the package cannot know, supplied by the user: the taxonomy (Family, Genus, Authority), the supporting-information block (Countries, Life Form, Substrate, Habitat, Biome, Vegetation), free-text land use and conservation units, a list of examined vouchers, a taxonomic reference (a Reflora / POWO link, or - for a newly described species - the article citation) and up to four photographs.

The whole page is self-contained (fonts fall back to the system stack, images and charts are embedded as base64 data URIs), so the returned file can be opened offline or published as-is (e.g. on GitHub Pages). Each photograph carries a watermark in its lower-right corner with the owner name given in photo_credit.

Usage

factsheet_html(
  assessment,
  species = NULL,
  lang = c("en", "pt"),
  file = NULL,
  family = NULL,
  genus = NULL,
  authority = NULL,
  countries = NULL,
  life_form = NULL,
  substrate = NULL,
  habitat = NULL,
  biome = NULL,
  vegetation = NULL,
  land_use = NULL,
  conservation_units = NULL,
  vouchers = NULL,
  reference = NULL,
  photos = NULL,
  photo_credit = NULL,
  cover_series = NULL,
  fire_series = NULL,
  applied_category = NULL,
  applied_code = NULL,
  map = TRUE,
  map_interactive = TRUE,
  top_n_threats = 5L
)

Arguments

assessment

A geoconv_assessment from assess_species.

species

Species name (default: the first assessed).

lang

Factsheet language: "en" (default) or "pt".

file

Optional output path. When supplied the HTML is written there and the path is returned invisibly; otherwise the HTML is returned as a length-one character string.

family, genus, authority

Taxonomy fields. genus defaults to the first word of species; the others are user-supplied (optional).

countries, life_form, substrate, habitat, biome, vegetation

The "Supporting information" block, all optional free text.

land_use, conservation_units

Optional overrides. When left NULL they are filled in automatically from the assessment: land_use from the anthropic land-cover classes within the EOO (the Conversion module) and conservation_units from the overlapping protected areas (the Protected-areas module). Pass a string to override the derived value; line breaks are preserved.

vouchers

Optional examined material: a character vector (one voucher per element) or a single string with one voucher per line.

reference

Optional taxonomic reference: a Reflora / POWO URL (rendered as a link) or, for a newly described taxon, the article citation.

photos

Optional character vector of image file paths (PNG/JPEG/...); at most the first four are used.

photo_credit

Watermark text (photo owner). A single value is applied to every photo; a vector is matched per photo.

cover_series, fire_series

Optional land-cover / burned-area time series for this species (as for assessment_report); when supplied they add the temporal-trend narrative and their charts (a land-cover composition-over-time chart, and a burned-area-per-year chart).

applied_category, applied_code

Optional applied Criterion B category (e.g. "VU") and full code (e.g. "VU B1ab(iii)"), reflecting the sub-criteria chosen by the user. When supplied they are shown as an "Applied Criterion B category" metric; otherwise the assessment's category_B / criterion_B_code columns are used if present.

map

Logical; embed the distribution map (occurrence points, EOO, AOO and land cover). Default TRUE; set FALSE to skip it (e.g. offline or for speed).

map_interactive

Logical; when TRUE (default) embed the interactive Leaflet map (map_species, the same widget the app downloads via "Download map (HTML)") as a self-contained document inside an iframe, so the whole factsheet remains one portable file. When FALSE, or when the widget cannot be built (no leaflet / htmlwidgets / pandoc), the publication-ready static map (map_static) is embedded instead.

top_n_threats

Number of anthropic land-cover classes to show in the "top anthropic activities" chart (default 5).

Value

The HTML string, or (when file is given) the file path, invisibly.

See also

assessment_report for the narrative-only report.

Examples

# \donttest{
occ <- read_occurrences(system.file("extdata", "example_occurrences.csv",
                                    package = "mappingAS"))
# reads MapBiomas (one year; the multi-year habitat trend is skipped)
res <- assess_species(occ, year = 2024, infer_decline_from_habitat = FALSE,
                      verbose = FALSE)
out <- file.path(tempdir(), "factsheet.html")
factsheet_html(res, file = out, map = FALSE,
               family = "Gentianaceae", countries = "Brazil",
               life_form = "Herb", biome = "Atlantic Forest")
unlink(out)
# }