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Biodiversity Specimen Data

a collection of specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions

This document provides a place to post links to code generally related to using biodiversity specimen data and hosted on an external source, e.g. your own GitHub repo, a lab website, etc.

Using the GloBi API via R to get species interaction data

Cleaning data in R - Presentation from ESA 2019 Data Help Desk, from Shelly Gaynor

Downloading specific columns from iDigBio, GBIF, and bison, from Shelly Gaynor

Materials from an Ecological Niche Modeling Workshop at Botany 2020, from the Soltis Lab

BiotaPhy. Species distribution and biodiversity modeling workflow environment.

Caviomorph Ecomorphology Resources. This app accompanies the manuscript Patterns in research and data-sharing for the study of form and function in caviomorph rodents to make data referenced in the paper accessible for exploration and reuse. See the app live here.

Introduction to GIS, including the use of in R. This repository provides an introduction to GIS and its application in biodiversity science. Written and maintained by Rhett Rautsaw.

R scripts for teaching course-based undergraduate research. Course material made for “CURE: Florida Plants and Climate Change” taught at the University of Florida in Spring 2020.

Spatial Ecology Workshop. Content from a 2018 workshop put together by University of Florida Biodiversity Informatics fellows.

Taxon Tools. Awk scripts for parsing and reconciling taxonomic names against a user-defined reference list. Written and maintained by Cam Webb.

TrIAS. Tools for standardizing thematic species checklist data to Darwin Core using R.