Resources
External guidance and tools that support GeoEpi work.
These links are useful starting points, not a policy catalog. Check the source page, current version, license, access conditions, and fit for your project before relying on a resource.
Data management
- USDA National Agricultural Library: Data Management Planning — primary conceptual source for the six-part project DMP structure used in this Lab Book.
- ICPSR: Share & Manage Data — secondary practical guidance on managing, documenting, sharing, and preserving research data.
- Ag Data Commons — a USDA data discovery and repository resource where appropriate.
GeoEpi tools and working systems
- SCINet — USDA scientific computing and storage context, including Atlas and Ceres.
- GitHub — GeoEpi organization and subproject repositories.
- Quarto — reproducible reports, websites, notebooks, and technical documentation.
- Overleaf — collaborative LaTeX documents and manuscripts.
- Zotero — shared literature management.
- OSF — collaborator-accessible research objects and project resources where appropriate.
The GeoEpi tools page explains the role of each system and the boundaries between them.
Online guides for analytical work
These online books, manuals, and course materials are useful references for analytical work commonly encountered in GeoEpi. They are learning resources, not prescribed methods; use the approach appropriate to the scientific question and data.
Ecology, population biology, and forecasting
- Primer of Ecology - ecological modeling and quantitative population concepts.
- Quantitative Biology - quantitative biology concepts and worked examples.
- A Practical Guide to Ecosystem Forecasting - ecological forecasting workflows.
- Forecasting: Principles and Practice - forecasting workflows with the forecast package in R.
Spatial analysis and geocomputation
- Spatial Data Science - spatial analysis workflows and concepts.
- R | Intro to GIS and Spatial Analysis - introductory GIS and spatial analysis in R.
- Spatial Data Processing with R - spatial data processing workflows in R.
- Geocomputation with R - geocomputation and spatial data science in R.
Statistics and comparative methods
- Rethinking - Bayesian statistical modeling and model reasoning.
- Comparative Methods - comparative methods and phylogenetic analysis concepts.
- Non-Gaussian Models in Stan - using CmdStanR interface to fit Stan models.
- Prior Choice Recommendations - Choosing Bayesian priors, especially in Stan.
Population, landscape, and computational genetics
- Landscape Genetic Data Analysis with R - population and landscape genetic analysis.
- Applied Population Genetics - applied population genetics workflows.
- Molecular Epi in R - molecular epidemiology analysis in R.
- Computational Genomics Manual - computational genomics methods and implementation.
Epidemiology
- The Epidemiologist R Handbook - applied epidemiological analysis in R.
Network analysis
- Network Analysis in R - network methods and implementation in R.
- Network Analysis: Integrating Social Network Theory, Method, and Application with R - network theory and applied analysis in R.
Causal analysis
- Causal Inference in R - answering causal questions using R.
Integrated Laplace Approximation
- Dynamic Time Series Models using R-INLA - use of an approximate Bayesian methods with R-INLA for dynamic modeling of time series.
- Spatial SPDE Models - spatial Modeling with Stochastic Partial Differential Equations Using R and INLA.
Software development, HPCs, and computer science
- Applied HPC with R - applied HPC with R is a collection of talks and lectures about speeding up your R code parallel computing and other resources.
- R Packages (2e) - 2nd edition of R Packages by Hadley Wickham. Functional programing and paackage design.