A collection of some resources that may be helpful or otherwise interesting...
Table of contents
- How and why to build R Packages
- Bob's (very incomplete but growing) list of open source datasets
- ENMeval (our R package for building and evaluating ecological niche models)
How and Why to Build R Packages
There are many reasons to learn to build R packages. They can help you organize your own projects, share code and data with collaborators, and provide useful tools to other researchers. I designed this tutorial to help demystify the process:
Download:
> Presentation PDF
> R script
> Build & check cheatsheet
Additional Resources:
> The official and essential guide from CRAN: "Writing R Extensions"
> David Diez provides excellent video guides: "Building Packages" ; and a great PDF: "Building R Pacakges"
> Hadley Wickham wrote a book (with a great website): "R Packages"
> R Studio has a blog guide: "Package Development"
> R.M. Ripley has a PDF guide: "Making an R package"
> Hilary Parker has a blog tutorial: "Writing an R Package from Scratch"
> Another great resource from David Diez: "Code performance and aesthetics in R"
> Iain Stott at the Methods in Ecology and Evolution Blog, "A Quickstart Guide for Building Your First R Package".
> Several other relevant resources from "The UCLA Statistical Consulting Center"
There are many reasons to learn to build R packages. They can help you organize your own projects, share code and data with collaborators, and provide useful tools to other researchers. I designed this tutorial to help demystify the process:
Download:
> Presentation PDF
> R script
> Build & check cheatsheet
Additional Resources:
> The official and essential guide from CRAN: "Writing R Extensions"
> David Diez provides excellent video guides: "Building Packages" ; and a great PDF: "Building R Pacakges"
> Hadley Wickham wrote a book (with a great website): "R Packages"
> R Studio has a blog guide: "Package Development"
> R.M. Ripley has a PDF guide: "Making an R package"
> Hilary Parker has a blog tutorial: "Writing an R Package from Scratch"
> Another great resource from David Diez: "Code performance and aesthetics in R"
> Iain Stott at the Methods in Ecology and Evolution Blog, "A Quickstart Guide for Building Your First R Package".
> Several other relevant resources from "The UCLA Statistical Consulting Center"
A very incomplete list of open source datasets
Publicly available datasets allow us to address many questions across scales that have not been possible before.
The list below is only a small sample of available resources, please feel free to email me with important additions!
Species occurrences and vegetation plots:
> Global Biodiversity Information Facility (GBIF)
> Biodiversity Information Serving "Our" Nation (BISON)
> Botanical Information and Ecology Network (BIEN)
> VegBank
> USFS Forest Inventory and Analysis (FIA)
Plant traits:
> TRY (plant trait database)
> Botanical Information and Ecology Network (BIEN)
Climate and environment:
> IRI/LDEO Climate data library
> Chelsa Climate data
> WorldClim (including BioClim)
> Harmonized World Soil Database
> Current and historical biomes (Harrison, S.P. 2017. BIOME 6000 DB classified plotfile version 1. University of Reading)
Human land use:
> Anthropogenic land use estimates for the Holocene (HYDE 3.2)
Population matrix models:
> Compadre (plants) & Comadre (animals)
(Phylo)genetic:
> TreeBase
> National Center for Biotechnology Information (including GenBank)
Publicly available datasets allow us to address many questions across scales that have not been possible before.
The list below is only a small sample of available resources, please feel free to email me with important additions!
Species occurrences and vegetation plots:
> Global Biodiversity Information Facility (GBIF)
> Biodiversity Information Serving "Our" Nation (BISON)
> Botanical Information and Ecology Network (BIEN)
> VegBank
> USFS Forest Inventory and Analysis (FIA)
Plant traits:
> TRY (plant trait database)
> Botanical Information and Ecology Network (BIEN)
Climate and environment:
> IRI/LDEO Climate data library
> Chelsa Climate data
> WorldClim (including BioClim)
> Harmonized World Soil Database
> Current and historical biomes (Harrison, S.P. 2017. BIOME 6000 DB classified plotfile version 1. University of Reading)
Human land use:
> Anthropogenic land use estimates for the Holocene (HYDE 3.2)
Population matrix models:
> Compadre (plants) & Comadre (animals)
(Phylo)genetic:
> TreeBase
> National Center for Biotechnology Information (including GenBank)
ENMeval
In collaboration with Dr. Rob Anderson's lab at City College of New York, I developed ENMeval, an R package for conducting spatially independent evaluations, estimating optimal model complexity, and evaluating Maxent ecological niche models. The tools in ENMeval greatly simplify the process of conducting species-specific tuning of Maxent models. We are continuing to develop ENMeval (e.g., expansion to other algorithms) so please send me suggestions of things you'd like to see in the next version.
Downloads & Resources:
> Download the package and manual from CRAN
> Check out our new vignette!
> Read the paper in Methods in Ecology & Evolution
> Visit the project on GitHub
In collaboration with Dr. Rob Anderson's lab at City College of New York, I developed ENMeval, an R package for conducting spatially independent evaluations, estimating optimal model complexity, and evaluating Maxent ecological niche models. The tools in ENMeval greatly simplify the process of conducting species-specific tuning of Maxent models. We are continuing to develop ENMeval (e.g., expansion to other algorithms) so please send me suggestions of things you'd like to see in the next version.
Downloads & Resources:
> Download the package and manual from CRAN
> Check out our new vignette!
> Read the paper in Methods in Ecology & Evolution
> Visit the project on GitHub
< broken links - under repair! >
SOFTWARE TOOLS
GitHub (Share and version control your code)
Software Carpentry (Learn the craft of code)
A Compendium of Clean R Graphs (Make nice graphs in R)
R Studio Cheatsheets!
Graphical Data Analysis in R (book with code!)
WEBSITE I'VE FOUND PARTICULARLY HELPFUL IN MY RESEARCH
AnthroTree (learn phylogenetics methods in R)
R Phylogenetics wiki (learn phylogenetics methods in R)
UConn CyberInfrastructure Course (Really nice SDM materials!)
TEACHING TOOLS
Evidence Based Teaching Network
Eberly Center (Resource for teaching and evaluation strategies)
The Plant Science TREE (Tool for Research Engaged Education)
Mentimeter online polls (Visualize real time responses from smartphones)
Kahoot (Create your own learning games...)
CARIBBEAN PLANT RESOURCES
Catalogue of the Seed Plants of the West Indies (Smithsonian)
A virtual flora for El Verde Field Station
Key to the plants of Guánica dry forest
Herbarium at the University of Puerto Rico, Río Piedras
Puerto Rico & Virgin Island Plant Conservation Task Force
USFS International Institute of Tropical Forestry (IITF)
Jimenez guide to Rainforest Plants
Native and Exotic Trees of Puerto Rico
A Systematic Vademecum to the Vascular Plants of Puerto Rico
ART & NATURE
Signal Fire Art Residency
The Center for Land Use Interpretation
SOME NICE THINGS IN PLACES I'VE LIVED
Aarhus, Denmark:
DOKK1: World's greatest public library!
Europe's Capital of Culture for 2017
New York City, NY, USA:
NYC Bike map
NYC Tree museum
NYC Books through Bars
WKCR Radio
Miami, FL, USA
Miami Art Basel
Gifford Arboretum
Fruit and Spice Museum
Fairchild Botanic Garden
Portland, OR, USA
BARK Forest Watchdog group
SOFTWARE TOOLS
GitHub (Share and version control your code)
Software Carpentry (Learn the craft of code)
A Compendium of Clean R Graphs (Make nice graphs in R)
R Studio Cheatsheets!
Graphical Data Analysis in R (book with code!)
WEBSITE I'VE FOUND PARTICULARLY HELPFUL IN MY RESEARCH
AnthroTree (learn phylogenetics methods in R)
R Phylogenetics wiki (learn phylogenetics methods in R)
UConn CyberInfrastructure Course (Really nice SDM materials!)
TEACHING TOOLS
Evidence Based Teaching Network
Eberly Center (Resource for teaching and evaluation strategies)
The Plant Science TREE (Tool for Research Engaged Education)
Mentimeter online polls (Visualize real time responses from smartphones)
Kahoot (Create your own learning games...)
CARIBBEAN PLANT RESOURCES
Catalogue of the Seed Plants of the West Indies (Smithsonian)
A virtual flora for El Verde Field Station
Key to the plants of Guánica dry forest
Herbarium at the University of Puerto Rico, Río Piedras
Puerto Rico & Virgin Island Plant Conservation Task Force
USFS International Institute of Tropical Forestry (IITF)
Jimenez guide to Rainforest Plants
Native and Exotic Trees of Puerto Rico
A Systematic Vademecum to the Vascular Plants of Puerto Rico
ART & NATURE
Signal Fire Art Residency
The Center for Land Use Interpretation
SOME NICE THINGS IN PLACES I'VE LIVED
Aarhus, Denmark:
DOKK1: World's greatest public library!
Europe's Capital of Culture for 2017
New York City, NY, USA:
NYC Bike map
NYC Tree museum
NYC Books through Bars
WKCR Radio
Miami, FL, USA
Miami Art Basel
Gifford Arboretum
Fruit and Spice Museum
Fairchild Botanic Garden
Portland, OR, USA
BARK Forest Watchdog group