Frequently Asked Questions

What is the JABOT?

JABOT is an online system for managing scientific collections housed in herbaria, research laboratory networks at botanical institutions, and living collections in botanical gardens. From a management perspective, it offers curators, sub-curators, and herbarium staff a variety of tools for administration, productivity monitoring, and report generation. The platform allows users to input and publish specimen data and images, with built-in features for analyzing and improving data quality.

What can I use jabotR for?

The jabotR package allows researchers and taxonomists to download, filter, and analyze plant specimen data from the JABOT. With dedicated functions, users can access large datasets in Darwin Core Format, explore taxonomic and geographic distributions, and summarize collections efficiently.

Can jabotR assess how well my herbarium is represented, or find missing species?

Yes. Beyond retrieving and filtering records, jabotR includes three analytical functions that compare any JABOT-hosted herbarium against the Flora e Funga do Brasil (FFB): jabot_gaps() identifies taxa missing from a collection, jabot_coverage() measures how much of the FFB checklist a herbarium already represents, and jabot_missing() narrows that comparison to a specific state or municipality and maps candidate collecting localities from the pooled JABOT network. Each produces a self-contained, interactive HTML report. See the How-To Articles for step-by-step tutorials.

How do I install jabotR?

Visit the Get Started guide for installation instructions from GitHub.

Is jabotR free to use?

Yes. jabotR is open source, licensed under the MIT License.

Is this website available in Portuguese?

Yes. Every page has an EN/PT toggle in the navigation bar. Once you switch languages, the choice is remembered for the rest of your visit — you won’t need to switch again as you navigate between pages.

What output can jabotR generate?

While jabotR itself does not generate formatted documents, it is designed for data retrieval and analysis. However, it integrates well with tools like Quarto and RMarkdown to produce documents, HTML pages, and interactive apps using filtered specimen data.

Who are the developers of jabotR?

Development is sponsored by JBRJ, FINEP, and CNPq. Main developers:

Domingos Cardoso (@DBOSlab)
Giulia C. Ottino

View the code and contribute on GitHub: https://github.com/DBOSlab/jabotR

Why the name jabotR?

The name pays tribute to the Rio de Janeiro Botanical Garden’s JABOT system for managing herbarium collections, while also making a clever nod to the R programming language. It reflects JBRJ’s national leadership in botanical research, now strengthened by reproducible and transparent data workflows.

Where can I report bugs or request features?

Submit issues on GitHub: jabotR Issues.

Where can I ask questions and discuss jabotR?

Join our community via GitHub Discussions to ask questions, suggest ideas, or help others.

How does jabotR relate to JABOT?

The jabotR package acts as a programmatic interface to query, retrieve, and explore data from JABOT and its partner collections. It enhances access, encourages reproducibility, and supports large-scale taxonomic and biogeographic studies.

Can my herbarium join the JABOT?

Yes. Herbarium curators can contact Luís Alexandre Estevão da Silva estevao@jbrj.gov.br to initiate data and image contributions. Participating herbaria receive support to digitize and publish their collections.

--- title: "Frequently Asked Questions" format: html: toc: true --- <style> body { position: relative; } .watermark { position: fixed; bottom: 50px; right: 50px; opacity: 0.15; z-index: -1; width: 400px; } .background-overlay { position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: rgba(255, 255, 255, 0.8); z-index: -1; } </style> <img src='/figures/jabot_original_logo.png' class='watermark' alt='jabot logo watermark'> ### What is the JABOT? JABOT is an online system for managing scientific collections housed in herbaria, research laboratory networks at botanical institutions, and living collections in botanical gardens. From a management perspective, it offers curators, sub-curators, and herbarium staff a variety of tools for administration, productivity monitoring, and report generation. The platform allows users to input and publish specimen data and images, with built-in features for analyzing and improving data quality. ### What can I use jabotR for? The `jabotR` package allows researchers and taxonomists to download, filter, and analyze plant specimen data from the [JABOT](https://jabot.jbrj.gov.br/v3/consulta.php). With dedicated functions, users can access large datasets in Darwin Core Format, explore taxonomic and geographic distributions, and summarize collections efficiently. ### Can jabotR assess how well my herbarium is represented, or find missing species? Yes. Beyond retrieving and filtering records, `jabotR` includes three analytical functions that compare any JABOT-hosted herbarium against the [Flora e Funga do Brasil (FFB)](https://floradobrasil.jbrj.gov.br/consulta/): `jabot_gaps()` identifies taxa missing from a collection, `jabot_coverage()` measures how much of the FFB checklist a herbarium already represents, and `jabot_missing()` narrows that comparison to a specific state or municipality and maps candidate collecting localities from the pooled JABOT network. Each produces a self-contained, interactive HTML report. See the [How-To Articles](/articles/index.qmd) for step-by-step tutorials. ### How do I install jabotR? Visit the [Get Started guide](/get-started/index.qmd) for installation instructions from GitHub. ### Is jabotR free to use? Yes. `jabotR` is open source, licensed under the [MIT License](https://opensource.org/license/mit/). ### Is this website available in Portuguese? Yes. Every page has an EN/PT toggle in the navigation bar. Once you switch languages, the choice is remembered for the rest of your visit — you won't need to switch again as you navigate between pages. ### What output can jabotR generate? While `jabotR` itself does not generate formatted documents, it is designed for data retrieval and analysis. However, it integrates well with tools like Quarto and RMarkdown to produce documents, HTML pages, and interactive apps using filtered specimen data. ### Who are the developers of jabotR? Development is sponsored by [JBRJ](https://www.gov.br/jbrj/pt-br), [FINEP](http://www.finep.gov.br), and [CNPq](https://www.gov.br/cnpq/pt-br). Main developers: - Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab)) - Giulia C. Ottino View the code and contribute on GitHub: [https://github.com/DBOSlab/jabotR](https://github.com/DBOSlab/jabotR) ### Why the name jabotR? The name pays tribute to the Rio de Janeiro Botanical Garden’s JABOT system for managing herbarium collections, while also making a clever nod to the R programming language. It reflects JBRJ’s national leadership in botanical research, now strengthened by reproducible and transparent data workflows. ### Where can I report bugs or request features? Submit issues on GitHub: [jabotR Issues](https://github.com/DBOSlab/jabotR/issues). ### Where can I ask questions and discuss jabotR? Join our community via [GitHub Discussions](https://github.com/DBOSlab/jabotR/discussions) to ask questions, suggest ideas, or help others. ### How does jabotR relate to JABOT? The `jabotR` package acts as a programmatic interface to query, retrieve, and explore data from JABOT and its partner collections. It enhances access, encourages reproducibility, and supports large-scale taxonomic and biogeographic studies. ### Can my herbarium join the JABOT? Yes. Herbarium curators can contact **Luís Alexandre Estevão da Silva <estevao@jbrj.gov.br>** to initiate data and image contributions. Participating herbaria receive support to digitize and publish their collections.