We live in the information age, unfortunately a lot of the information we want is buried deep in the internet. If you are just starting out with GIS, R, or large data sets, it seems like the right help is kept in an even more remote cavity. Below are some sources I have found helpful as I explore macroecology. If you have any other recommendations, leave them in the comments section.
R Tutorial – For the basics of working with R, don’t neglect indexing
Adv. R – Getting farther along
Reshape2 – Dirty data set? Clean it up with Reshape2. Sean Anderson does a great job explaining this package
Vegan tutorial – This package is great for community ecology and describing multidimensional data sets.
Spatial.ly – If you want to use R as a GIS this website provides a good starting point
Various Topics in Ecology – Max Joseph is a 5th year graduate student at CU-Boulder who writes interesting code/posts
GBIF – For getting data sets from museum collections – use their R package for faster data processing
Discoverlife – For Identifying bees and getting natural history information
Bee Basics – An overview of bees
USGS Data Gateway – Click the green button and explore the possibilities of government funded spatial data
Colorado GIS data repository – Pretty much every state has one, wikipedia has a nice list of global GIS databases