iDigBio API info

• iDigBio API overview
• iDigBio Search API documentation
• iDigBio R package
• iDigBio Python library

R packages we like

Essential R packages

• tidyverse: must-have suite of packages for data wrangling and analysis that includes many other packages, e.g.:
  • dplyr for data management
  • tidyr for tidying your data
  • ggplot2 for data visualization
  • stringr for string filtering and manipulation (recommended by @frog_phylo)

R packages for biodiversity informatics

• bdchecks: performs data check for biodiversity data
• bdclean: cleans biodiversity data
• bddwc: standardizes data to Darwin Core (DwC) format
• bdverse: suite of packages to facilitate biodiversity science for “inexperienced R users”
• BIEN: access to the Botanical Information and Ecology Network database; see tutorial
• coordinatecleaner: spatial and temporal data quality
• rgbif: access to data from GBIF via the GBIF API
• ridigbio: access to data from the iDigBio Portal via the iDigBio API
• scrubr: biodiversity occurrence data quality
• spocc: access to multiple biodiversity occurrence sources, including the iDigBio Portal and GBIF, via APIs
• spThin: tools for reducing spatial sampling bias of occurrence records (recommended by @maverickpandion)
• taxize: access to multiple taxonomic data sources via APIs
• taxizedb: access to taxonomic data sources via local database
• wallace: “R-based platform for reproducible modeling of species niches and distributions”; note that this requires rJava

Other Important R packages

• biogeo: spatial data quality
• checkpoint: managing packages for reproducibility
• dismo: species distribution modeling
• ggmap: geospatial analysis
• knitr: report generation from RMarkdown code
• lubridate: for cleaning and converting dates
• packrat: managing packages
• rOpenSci: “Our packages are carefully vetted, staff- and community-contributed R software tools that lower barriers to working with scientific data sources and data that support research applications on the web”

Links for more learning

• Twitter for R programmers
• The Carpentries: “The Carpentries teaches foundational coding, and data science skills to researchers worldwide.” This organization hosts workshops and makes its lesson plans available freely for self-learning and reuse. Main lessons are divided into…
  • Software Carpentry
  • Data Carpentry
  • Library Carpentry
• Hadley Wickham’s (of the Tidyverse) site with online books
• O’Reilly Head First Programming series
• Datacamp paid online courses
• Tidyverse style guide for code
• Unit testing for R
• Background reading on unit testing for R

Non-R tools:

• OpenRefine: can be used to clean data (ex. Baldwin et al. 2017).
• Biodiverse: “tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations”
• Glosario: A glossary of terms related to programming, designed for beginnings to reference