News

jabotR 1.0.0

Initial Release

The first official release of the jabotR R package, designed to streamline access to plant specimen data from the JABOT online herbarium collections, hosted by the Rio de Janeiro Botanical Garden.

Features

jabot_summary(): Retrieve metadata and summary info from all or specific JABOT herbaria.
jabot_download(): Download original specimen data in Darwin Core Archive (DwC-A) format.
jabot_parse(): Read and parse downloaded Darwin Core Archive files into R.
jabot_records(): Retrieve, filter, and organize JABOT specimen records by taxon, herbarium, region, and year.
jabot_indets(): Retrieve indeterminate specimens (e.g., identified only to family or genus rank).
jabot_gaps(): Identify taxa missing from a herbarium relative to the Flora e Funga do Brasil, with an optional nationwide, municipality-level collecting-priority heat map (priority_map).
jabot_coverage(): Measure how well a herbarium represents the Flora e Funga do Brasil, by taxonomic group, family, phytogeographic domain, and Brazilian state.
jabot_missing(): Identify species expected in a target Brazilian state/municipality that are missing from a local herbarium, with an interactive map of candidate collecting localities and a municipality-level collecting-priority heat map drawn from the pooled JABOT network — including direct links to physical specimen images when available.
jabot_identify(): Suggest identifications for the indeterminate specimens of a herbarium (lacking family, genus, or specific epithet) by finding their duplicates in the whole JABOT network and in REFLORA (via refloraR) with barRoso, with an optional taxon filter, support for REFLORA-only herbaria, and an interactive HTML report listing the suggested identification, its source herbarium and specimen link, and conflicts between duplicates.
jabot_fieldbook(): Open an offline field notebook in the browser to organize collection events and specimens and export a standardized 58-column JABOT spreadsheet and a printable field notebook in PDF format.
jabot_gaps(), jabot_coverage(), and jabot_missing() each produce a self-contained, interactive HTML report.
Optional filters by taxon, herbarium, state, recordYear, and level.
Supports integration with tidyverse workflows for downstream analyses.
Comprehensive testthat suite, continuous integration via GitHub Actions.

Infrastructure

MIT license.
GitHub Actions: R-CMD-check and test coverage.
Hosted documentation: jabotR-website, with How-To articles for every function and a full Portuguese translation (EN/PT language switcher).

Feedback

Please report bugs or issues at: https://github.com/DBOSlab/jabotR/issues

--- title: "News" format: html: toc: true toc-depth: 3 --- <style> body { position: relative; } .watermark { position: fixed; bottom: 50px; right: 50px; opacity: 0.15; z-index: -1; width: 400px; } </style> <img src="/figures/jabot_original_logo.png" class="watermark" alt="jabot logo watermark"> # jabotR 1.0.0 ## Initial Release The first official release of the `jabotR` R package, designed to streamline access to plant specimen data from the [JABOT online herbarium collections](https://jabot.jbrj.gov.br/v3/consulta.php), hosted by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj/pt-br). ### Features - `jabot_summary()`: Retrieve metadata and summary info from all or specific JABOT herbaria. - `jabot_download()`: Download original specimen data in Darwin Core Archive (DwC-A) format. - `jabot_parse()`: Read and parse downloaded Darwin Core Archive files into R. - `jabot_records()`: Retrieve, filter, and organize JABOT specimen records by taxon, herbarium, region, and year. - `jabot_indets()`: Retrieve indeterminate specimens (e.g., identified only to family or genus rank). - `jabot_gaps()`: Identify taxa missing from a herbarium relative to the Flora e Funga do Brasil, with an optional nationwide, municipality-level collecting-priority heat map (`priority_map`). - `jabot_coverage()`: Measure how well a herbarium represents the Flora e Funga do Brasil, by taxonomic group, family, phytogeographic domain, and Brazilian state. - `jabot_missing()`: Identify species expected in a target Brazilian state/municipality that are missing from a local herbarium, with an interactive map of candidate collecting localities and a municipality-level collecting-priority heat map drawn from the pooled JABOT network — including direct links to physical specimen images when available. - `jabot_identify()`: Suggest identifications for the indeterminate specimens of a herbarium (lacking family, genus, or specific epithet) by finding their duplicates in the whole JABOT network and in REFLORA (via `refloraR`) with `barRoso`, with an optional `taxon` filter, support for REFLORA-only herbaria, and an interactive HTML report listing the suggested identification, its source herbarium and specimen link, and conflicts between duplicates. - `jabot_fieldbook()`: Open an offline field notebook in the browser to organize collection events and specimens and export a standardized 58-column JABOT spreadsheet and a printable field notebook in PDF format. - `jabot_gaps()`, `jabot_coverage()`, and `jabot_missing()` each produce a self-contained, interactive HTML report. - Optional filters by `taxon`, `herbarium`, `state`, `recordYear`, and `level`. - Supports integration with tidyverse workflows for downstream analyses. - Comprehensive testthat suite, continuous integration via GitHub Actions. ### Infrastructure - MIT license. - GitHub Actions: R-CMD-check and test coverage. - Hosted documentation: [jabotR-website](https://dboslab.github.io/jabotR-website/), with How-To articles for every function and a full Portuguese translation (EN/PT language switcher). ### Feedback Please report bugs or issues at: <https://github.com/DBOSlab/jabotR/issues>