jabot_coverage

Herbarium representativeness within the Flora e Funga do Brasil

jabotR::jabot_coverage()

Description

Measures how well a JABOT-hosted herbarium represents the Flora e Funga do Brasil (FFB). Unlike jabot_gaps (which focuses on what is missing), this function characterises what is present, computing coverage ratios at every taxonomic and geographic level:

Overall representativeness (% of FFB species held in the herbarium)
Coverage by group, family, and phytogeographic domain
Family-level bar charts ranked by coverage (best- and worst-covered)
Choropleth map of % coverage by Brazilian state
Summary statistics table
An HTML report (always generated) and optional PDF / PNG exports of every individual figure

Details

Coverage is defined as: =

The function follows the same data-preparation pipeline as jabot_gaps: FFB data are parsed, JABOT records fetched, and synonym names resolved before the comparison is made.

Arguments

Argument	Description
herbarium	Character. Herbarium acronym in uppercase (e.g. `"RB"`).
jabot_path	Character or `NULL`. Path to a directory holding previously downloaded JABOT DwC-A files. When `NULL` (default) the records are downloaded automatically via `jabot_download`.
format	Character vector. Static formats for saving individual figures: `"pdf"`, `"png"`, or both. The HTML report is always generated.
fig_width	Numeric. Width of saved figures in inches. Default `10`.
fig_height	Numeric. Height of saved figures in inches. Default `6`.
open_report	Logical. If `TRUE` (default), opens the HTML report in the default browser after rendering.
verbose	Logical. If `TRUE` (default), progress messages are printed.
dir	Character. Output directory. Defaults to `"<herbarium>_representativeness"`.

Value

Invisibly returns a named list with all computed data frames and ggplot2 objects. The HTML report (and optional figures) are written to dir.

Examples

# Full run - renders HTML and saves PDF figures
jabot_coverage(herbarium = "RB",
               format = "pdf",
               dir = "RB_representativeness")

# Re-run using cached data
jabot_coverage(herbarium = "RB",
               jabot_path = "jabot_download",
               format = c("pdf", "png"))

--- title: 'jabot_coverage' description: 'Herbarium representativeness within the Flora e Funga do Brasil' toc: true toc-depth: 3 --- ```{r} #| eval: false jabotR::jabot_coverage() ``` ### Description Measures how well a JABOT-hosted herbarium represents the [Flora e Funga do Brasil (FFB)](https://floradobrasil.jbrj.gov.br/consulta/). Unlike `jabot_gaps` (which focuses on what is missing), this function characterises what is present, computing coverage ratios at every taxonomic and geographic level: - Overall representativeness (% of FFB species held in the herbarium) - Coverage by group, family, and phytogeographic domain - Family-level bar charts ranked by coverage (best- and worst-covered) - Choropleth map of % coverage by Brazilian state - Summary statistics table - An HTML report (always generated) and optional PDF / PNG exports of every individual figure ### Details Coverage is defined as: \text{coverage} = \frac{N_{\text{in herbarium}}}{N_{\text{FFB total}}} \times 100 The function follows the same data-preparation pipeline as `jabot_gaps`: FFB data are parsed, JABOT records fetched, and synonym names resolved before the comparison is made. ### Arguments | Argument | Description | |---|---| | herbarium | Character. Herbarium acronym in uppercase (e.g. `"RB"`). | | jabot_path | Character or `NULL`. Path to a directory holding previously downloaded JABOT DwC-A files. When `NULL` (default) the records are downloaded automatically via `jabot_download`. | | format | Character vector. Static formats for saving individual figures: `"pdf"`, `"png"`, or both. The HTML report is always generated. | | fig_width | Numeric. Width of saved figures in inches. Default `10`. | | fig_height | Numeric. Height of saved figures in inches. Default `6`. | | open_report | Logical. If `TRUE` (default), opens the HTML report in the default browser after rendering. | | verbose | Logical. If `TRUE` (default), progress messages are printed. | | dir | Character. Output directory. Defaults to `"<herbarium>_representativeness"`. | ### Value Invisibly returns a named list with all computed data frames and ggplot2 objects. The HTML report (and optional figures) are written to `dir`. ### Examples ```r # Full run - renders HTML and saves PDF figures jabot_coverage(herbarium = "RB", format = "pdf", dir = "RB_representativeness") # Re-run using cached data jabot_coverage(herbarium = "RB", jabot_path = "jabot_download", format = c("pdf", "png")) ```